More stories

  • in

    Birds adapted to cold conditions show greater changes in range size related to past climatic oscillations than temperate birds

    Hewitt, G. M. The genetic legacy of the Quaternary ice ages. Nature 405, 907–913 (2000).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Drovetski, S. V. et al. A test of the European Pleistocene refugial paradigm, using a Western Palaearctic endemic bird species. Proc. R. Soc. B 285, 20181606 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hewitt, G. M. Quaternary phylogeography: the roots of hybrid zones. Genetica 139, 617–638 (2011).PubMed 
    Article 

    Google Scholar 
    Nadachowska-Brzyska, K., Li, C., Smeds, L., Zhang, G. & Ellegren, H. Temporal dynamics of avian populations during Pleistocene revealed by whole-genome sequences. Curr. Biol. 25, 1375–1380 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Newton, I. Speciation and Biogeography of Birds (Academic Press, 2003).
    Google Scholar 
    Pellegrino, I. et al. Phylogeography and Pleistocene refugia of the Little Owl Athene noctua inferred from mtDNA sequence data. Ibis 156, 639–657 (2014).Article 

    Google Scholar 
    Tietze, D. T. Bird Species: How they Arise, Modify and Vanish (Springer Nature, 2018).Book 

    Google Scholar 
    Carrera, L., Pavia, M., Peresani, M. & Romandini, M. Late Pleistocene fossil birds from Buso Doppio del Broion Cave (North-Eastern Italy): implications for palaeoecology, palaeoenvironment and palaeoclimate. Boll. Soc. Paleontol. I(57), 145–174 (2018).
    Google Scholar 
    Carrera, L., Pavia, M., Romandini, M. & Peresani, M. Avian fossil assemblages at the onset of the LGM in the eastern Alps: a palaecological contribution from the Rio Secco Cave (Italy). C. R. Palevol 17, 166–177 (2018).Article 

    Google Scholar 
    Carrera, L., Scarponi, D., Martini, F., Sarti, L. & Pavia, M. Mid-Late Pleistocene Neanderthal landscapes in southern Italy: paleoecological contributions of the avian assemblage from Grotta del Cavallo, Apulia, southern Italy. Palaeogeogr. Palaeocl. 567, 110256 (2021).Article 

    Google Scholar 
    Clark, P. U. et al. The last glacial maximum. Science 325, 710–714 (2009).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Hampe, A. & Jump, A. S. Climate relicts: past, present, future. Annu. Rev. Ecol. Evol. S. 42, 313–333 (2011).Article 

    Google Scholar 
    Holm, S. R. & Svenning, J. C. 180,000 years of climate change in Europe: avifaunal responses and vegetation implications. PLoS ONE 9, e94021 (2014).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    Sanchez Marco, A. Avian zoogeographical patterns during the Quaternary in the Mediterranean region and paleoclimatic interpretation. Ardeola 51, 91–132 (2004).
    Google Scholar 
    Elith, J. & Leathwick, J. R. Species distribution models: ecological explanation and prediction across space and time. Annu. Rev. Ecol. Evol. S. 40, 677–697 (2009).Article 

    Google Scholar 
    Gavin, D. G. et al. Climate refugia: joint inference from fossil records, species distribution models and phylogeography. New Phytol. 204, 37–54 (2014).PubMed 
    Article 

    Google Scholar 
    Nogués-Bravo, D. Predicting the past distribution of species climatic niches. Glob. Ecol. Biogeogr. 18, 521–531 (2009).Article 

    Google Scholar 
    Svenning, J. C., Fløjgaard, C., Marske, K. A., Nogues-Bravo, D. & Normand, S. Applications of species distribution modeling to paleobiology. Quat. Sci. Rev. 30, 2930–2947 (2011).Article 
    ADS 

    Google Scholar 
    Varela, S., Lobo, J. M. & Hortal, J. Using species distribution models in paleobiogeography: a matter of data, predictors and concepts. Palaeogeogr. Palaeocl. 310, 451–463 (2011).Article 

    Google Scholar 
    Arcones, A., Ponti, R., Ferrer, X. & Vieites, D. R. Pleistocene glacial cycles as drivers of allopatric differentiation in Arctic shorebirds. J. Biogeogr. 48, 747–759 (2021).Article 

    Google Scholar 
    Kozma, R., Melsted, P., Magnússon, K. P. & Höglund, J. Looking into the past–the reaction of three grouse species to climate change over the last million years using whole genome sequences. Mol. Ecol. 25, 570–580 (2016).PubMed 
    Article 

    Google Scholar 
    Lagerholm, V. K. et al. Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds. Glob. Change Biol. 23, 1425–1435 (2017).Article 
    ADS 

    Google Scholar 
    Metcalf, J. L. et al. Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study. Proc. R. Soc. B 281, 20132782. https://doi.org/10.1098/rspb.2013.2782 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Perktaş, U., Peterson, A. T. & Dyer, D. Integrating morphology, phylogeography, and ecological niche modeling to explore population differentiation in North African Common Chaffinches. J. Ornithol. 158, 1–13 (2017).Article 

    Google Scholar 
    Perktaş, U., De Silva, T. N., Quintero, E. & Tavşanoğlu, Ç. Adding ecology into phylogeography: ecological niche models and phylogeography in tandem reveals the demographic history of the subalpine warbler complex. Bird Study 66, 234–242 (2019).Article 

    Google Scholar 
    Fløjgaard, C., Normand, S., Skov, F. & Svenning, J. C. Ice age distributions of European small mammals: insights from species distribution modelling. J. Biogeogr. 36, 1152–1163 (2009).Article 

    Google Scholar 
    Lima-Ribeiro, M. S., Varela, S., Nogués-Bravo, D. & Diniz-Filho, J. A. F. Potential suitable areas of giant ground sloths dropped before its extinction in South America: the evidences from bioclimatic envelope modeling. Nat. Conserv. 10, 145–151 (2012).Article 

    Google Scholar 
    Lorenzen, E. D. et al. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479, 359–364 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Martínez-Meyer, E., Townsend Peterson, A. & Hargrove, W. W. Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity. Glob. Ecol. Biogeogr. 13, 305–314 (2004).Article 

    Google Scholar 
    Nogués-Bravo, D., Rodríguez, J., Hortal, J., Batra, P. & Araújo, M. B. Climate change, humans, and the extinction of the woolly mammoth. PLoS Biol. 6, e79 (2008).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Waltari, E. et al. Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS ONE 2, e563 (2007).PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Barrientos, R. et al. Refugia, colonization and diversification of an arid-adapted bird: coincident patterns between genetic data and ecological niche modelling. Mol. Ecol. 23, 390–407 (2014).PubMed 
    Article 

    Google Scholar 
    Huntley, B. & Green, R. E. Bioclimatic models of the distributions of Gyrfalcons and ptarmigan. In Gyrfalcons and Ptarmigan in a Changing World Vol. II (eds Watson, R. T. et al.) 329–338 (The Peregrine Fund, 2011).
    Google Scholar 
    Huntley, B., Allen, J. R. M., Barnard, P., Collingham, Y. C. & Holliday, P. R. Species distribution models indicate contrasting late-Quaternary histories for Southern and Northern Hemisphere bird species. Glob. Ecol. Biogeogr. 22, 277–288 (2013).Article 

    Google Scholar 
    Kiss, O. et al. Past and future climate-driven shifts in the distribution of a warm-adapted bird species, the European Roller Coracias garrulus. Bird Study 67, 143–159 (2020).Article 

    Google Scholar 
    Koparde, P., Mehta, P., Mukherjee, S. & Robin, V. V. Quaternary climatic fluctuations and resulting climatically suitable areas for Eurasian owlets. Ecol. Evol. 9, 4864–4874 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Peterson, A. T. & Ammann, C. M. Global patterns of connectivity and isolation of populations of forest bird species in the late Pleistocene. Glob. Ecol. Biogeogr. 22, 596–606 (2013).Article 

    Google Scholar 
    Peterson, A. T., Martínez-Meyer, E. & González-Salazar, C. Reconstructing the Pleistocene geography of the Aphelocoma jays (Corvidae). Divers. Distrib. 10, 237–246 (2004).Article 

    Google Scholar 
    Ponti, R., Arcones, A., Ferrer, X. & Vieites, D. R. Lack of evidence of a Pleistocene migratory switch in current bird long-distance migrants between Eurasia and Africa. J. Biogeogr. 47, 1564–1573 (2020).Article 

    Google Scholar 
    Ruegg, K. C., Hijmans, R. J. & Moritz, C. Climate change and the origin of migratory pathways in the Swainson’s thrush Catharus ustulatus. J. Biogeogr. 33, 1172–1182 (2006).Article 

    Google Scholar 
    Smith, S. E., Gregory, R. D., Anderson, B. J. & Thomas, C. D. The past, present and potential future distributions of cold-adapted bird species. Divers. Distrib. 19, 352–362 (2013).Article 

    Google Scholar 
    Sutton, L. J. et al. Geographic range estimates and environmental requirements for the harpy eagle derived from spatial models of current and past distribution. Ecol. Evol. 11, 481–497 (2021).PubMed 
    Article 

    Google Scholar 
    Varela, S., Lima-Ribeiro, M. S., Diniz-Filho, J. A. F. & Storch, D. Differential effects of temperature change and human impact on European Late Quaternary mammalian extinctions. Glob. Change Biol. 21, 1475–1481 (2015).Article 
    ADS 

    Google Scholar 
    Scridel, D. et al. Thermal niche predicts recent changes in range size for bird species. Clim. Res. 73, 207–216 (2017).Article 

    Google Scholar 
    Barnagaud, J. Y. et al. Relating Habitat and Climatic Niches in Birds. PLoS Biol. 7, e32819 (2012).CAS 
    ADS 

    Google Scholar 
    Devictor, V., Julliard, R., Jiguet, F. & Couvet, D. Birds are tracking climate warming, but not fast enough. Proc. R. Soc. Lond. [Biol.] 275, 2743–2748 (2008).
    Google Scholar 
    Gaüzère, P., Jiguet, F. & Devictor, V. Rapid adjustment of bird community compositions to local climatic variations and its functional consequences. Glob. Change Biol. 21, 3367–3378 (2015).Article 
    ADS 

    Google Scholar 
    Jiguet, F., Gadot, A., Julliard, R., Newson, S. & Couvet, D. Climate envelope, life history traits and the resilience of birds facing global change. Glob. Change Biol. 13, 1673–1685 (2007).Article 
    ADS 

    Google Scholar 
    Jiguet, F. et al. Bird population trends are linearly affected by climate change along species thermal ranges. Proc. R. Soc. Lond. [Biol.] 277, 3601–3608 (2010).
    Google Scholar 
    Jiguet, F. et al. Population trends of European common birds are predicted by characteristics of their climatic niche. Glob. Change Biol. 16, 497–505 (2010).Article 
    ADS 

    Google Scholar 
    Lindström, Å., Green, M., Paulson, G., Smith, H. G. & Devictor, V. Rapid changes in bird community composition at multiple temporal and spatial scales in response to recent climate change. Ecography 36, 313–322 (2013).Article 

    Google Scholar 
    Pearce-Higgins, J. W., Eglington, S. M., Martay, B. & Chamberlain, D. E. Drivers of climate change impacts on bird communities. J. Anim. Ecol. 84, 943–954 (2015).PubMed 
    Article 

    Google Scholar 
    Stephens, P. A. et al. Consistent response of bird populations to climate change on two continents. Science 352, 84–87 (2016).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    BirdLife International. Crex crex. The IUCN Red List of Threatened Species 2016: e.T22692543A86147127. https://dx.doi.org/https://doi.org/10.2305/IUCN.UK.2016-3.RLTS.T22692543A86147127.en (2016).BirdLife International. Perdix perdix. The IUCN Red List of Threatened Species 2016: e.T22678911A85929015. https://dx.doi.org/https://doi.org/10.2305/IUCN.UK.2016-3.RLTS.T22678911A85929015.en (2016).BirdLife International. Pyrrhocorax graculus. The IUCN Red List of Threatened Species 2016: e.T22705921A87386602. https://dx.doi.org/https://doi.org/10.2305/IUCN.UK.2016-3.RLTS.T22705921A87386602.en (2016).BirdLife International. Coturnix coturnix. The IUCN Red List of Threatened Species 2018: e.T22678944A131904485. https://dx.doi.org/https://doi.org/10.2305/IUCN.UK.2018-2.RLTS.T22678944A131904485.en (2018).BirdLife International. Athene noctua. The IUCN Red List of Threatened Species 2019: e.T22689328A155470112. https://dx.doi.org/https://doi.org/10.2305/IUCN.UK.2019-3.RLTS.T22689328A155470112.en (2019).BirdLife International. Bubo scandiacus. The IUCN Red List of Threatened Species 2020: e.T22689055A181375387. https://dx.doi.org/https://doi.org/10.2305/IUCN.UK.2020-3.RLTS.T22689055A181375387.en (2020).Cramp, S. The Complete Birds of the Western Palearctic on CD-ROM (Oxford University Press, 1998).
    Google Scholar 
    Tyrberg, T. Pleistocene Birds of the Palearctic: A Catalogue. (Publications of the Nuttall Ornithological Club No. 27, 1998).Tyrberg, T. Pleistocene Birds of the Palaearctic. http://web.telia.com/~u11502098/pleistocene.pdf (2008).Pellegrino, I. et al. Evidence for strong genetic structure in European populations of the little owl Athene noctua. J. Avian Biol. 46, 462–475 (2015).Article 

    Google Scholar 
    van Nieuwenhuyse, D., Génot, J. C. & Johnson, D. H. The Little Owl: Conservation, Ecology and Behavior of Athene noctua (Cambridge University Press, 2008).
    Google Scholar 
    Dupont, L. M. Vegetation zones in NW Africa during the Brunhes chron reconstructed from marine palynological data. Quat. Sci. Rev. 12, 189–202 (1993).Article 
    ADS 

    Google Scholar 
    Hoag, C. & Svenning, J. C. African environmental change from the Pleistocene to the Anthropocene. Annu. Rev. Env. Resour. 42, 27–54 (2017).Article 

    Google Scholar 
    Hoelzmann, P. et al. Palaeoenvironmental changes in the arid and sub arid belt (Sahara-Sahel-Arabian Peninsula) from 150 kyr to present. In Past Climate Variability Through Europe and Africa (eds Battarbee, R. W. et al.) 219–256 (Springer, 2004).Chapter 

    Google Scholar 
    Larrasoaña, J. C., Roberts, A. P. & Rohling, E. J. Dynamics of green Sahara periods and their role in hominin evolution. PLoS ONE 8, e76514 (2013).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    Bech, N., Novoa, C., Allienne, J. F., Boissier, J. & Bro, E. Quantifying genetic distance between wild and captive strains of the grey partridge Perdix perdix in France: conservation implications. Biodivers. Conserv. 29, 609–624 (2020).Article 

    Google Scholar 
    Liukkonen-Anttila, T., Uimaniemi, L., Orell, M. & Lumme, J. Mitochondrial DNA variation and the phylogeography of the grey partridge (Perdix perdix) in Europe: from Pleistocene history to present day populations. J. Evolut. Biol. 15, 971–982 (2002).CAS 
    Article 

    Google Scholar 
    Potapova, O. Snowy owl Nyctea scandiaca (Aves: Strigiformes) in the Pleistocene of the Ural Mountains with notes on its ecology and distribution in the Northern Palearctic. Deinsea 8, 103–126 (2001).
    Google Scholar 
    Mourer-Chauviré, C. Les oiseaux du Pléistocène moyen et supérieur de France. Doc. Lab. Géol. Fac. Sci. Lyon 64, 1–624 (1975).
    Google Scholar 
    Mourer-Chauviré, C. Les oiseaux dans les habitats pale´olithiques: gibier des hommes ou proies des rapaces? In Animal and Archaeology: 2. Shell Middens, Fishes and Birds (eds Grigson, C. & Clutton-Brock, J.) 111–124 (British Archaeological Reports International Series 183, 1983).
    Google Scholar 
    Meijer, H. J., Pavia, M., Madurell-Malapeira, J. & Alba, D. M. A revision of fossil eagle owls (Aves: Strigiformes: Bubo) from Europe and the description of a new species, Bubo ibericus, from Cal Guardiola (NE Iberian Peninsula). Hist. Biol. 29, 822–832 (2017).Article 

    Google Scholar 
    Sanchez Marco, A. Aves fósiles de la Península Ibérica, Canarias y Baleares: balance de los estudios realizados. Investig. Rev. PH Inst. Andal. Patrim. Hist. 94, 154–181 (2018).
    Google Scholar 
    Sardella, R. et al. Grotta Romanelli (Southern Italy, Apulia): legacies and issues in excavating a key site for the Pleistocene of the Mediterranean. Riv. Ital. Paleontol. S. 124, 247–264 (2018).
    Google Scholar 
    Rustioni, M., Ferretti, M. P., Mazza, P., Pavia, M. & Varola, A. The vertebrate fauna from Cardamone (Apulia, southern Italy): an example of Mediterranean mammoth fauna. Deinsea 9, 395–404 (2003).
    Google Scholar 
    Bedetti, C. & Pavia, M. Reinterpretation of the Late Pleistocene Ingarano Cave deposit based on the fossil bird association (Apulia, South-eastern Italy). Riv. Ital. Paleontol. S. 113, 487–507 (2007).
    Google Scholar 
    Tyrberg, T. Arctic, montane and steppe birds as glacial relicts in West Palearctic. Ornithol. Verh. 25, 29–49 (1991).
    Google Scholar 
    Bruderer, B. & Salewski, V. Evolution of bird migration in a biogeographical context. J. Biogeogr. 35, 1951–1959 (2008).Article 

    Google Scholar 
    Finlayson, C. Avian Survivors. The History and Biogeography of Palearctic Birds (T. & A.D. Poyser, 2011).
    Google Scholar 
    Louchart, A. Emergence of long distance bird migrations: a new model integrating global climate changes. Naturwissenschaften 95, 1109–1119 (2008).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Winger, B. M., Auteri, G. G., Pegan, T. M. & Weeks, B. C. A long winter for the Red Queen: rethinking the evolution of seasonal migration. Biol. Rev. 94, 737–752 (2019).PubMed 
    Article 

    Google Scholar 
    Somveille, M. et al. Simulation-based reconstruction of global bird migration over the past 50,000 years. Nat. Commun. 11, 1–9 (2020).Article 
    CAS 

    Google Scholar 
    Fiedler, W. Recent changes in migratory behaviour of birds: a compilation of field observations and ringing data. In Avian Migration (eds Berthold, P. et al.) 21–38 (Springer, 2003).Chapter 

    Google Scholar 
    Milá, B., Smith, T. B. & Wayne, R. K. Postglacial population expansion drives the evolution of long-distance migration in a songbird. Evolution 60, 2403–2409 (2006).PubMed 
    Article 

    Google Scholar 
    Zink, R. M. The evolution of avian migration. Biol. J. Linn. Soc. 104, 237–250 (2011).Article 

    Google Scholar 
    Zink, R. M. & Gardner, A. S. Glaciation as a migratory switch. Sci. Adv. 3, e1603133 (2017).PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Matthiesen, D. G. Avian medullary bone in the fossil record, an example from the Early Pleistocene of Olduvai Gorge, Tanzania. J. Vertebr. Paleontol. 9, 34A (1990).
    Google Scholar 
    Ponti, R., Arcones, A., Ferrer, X. & Vieites, D. R. Seasonal climatic niches diverge in migratory birds. Ibis 162, 318–330 (2020).Article 

    Google Scholar 
    Cohen, K. M. & Gibbard, P. L. Global chronostratigraphical correlation table for the last 2.7 million years, version 2019 QI-500. Quat. Int. 500, 20–31 (2019).Article 

    Google Scholar 
    Lisiecki, L. E. & Raymo, M. E. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20, PA1003. https://doi.org/10.1029/2004PA001071 (2005).Article 
    ADS 

    Google Scholar 
    Vermeersch, P. M. Radiocarbon Palaeolithic Europe Database, Version 26. https://ees.kuleuven.be/geography/projects/14c-palaeolithic/index.html (2019).d’Errico, F., Banks, W. E., Vanhaeren, M., Laroulandie, V. & Langlais, M. PACEA geo-referenced radiocarbon database. Paleoanthropology https://doi.org/10.4207/PA.2011.ART40 (2011).Article 

    Google Scholar 
    Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360. https://doi.org/10.1017/S0033822200033865 (2009).Article 

    Google Scholar 
    Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 years cal BP. Radiocarbon 55, 1869–1897. https://doi.org/10.2458/azu_js_rc.55.16947 (2013).CAS 
    Article 

    Google Scholar 
    Serjeantson, D. Birds: a seasonal resource. Environ. Archaeol. 3, 23–33 (1998).Article 

    Google Scholar 
    Serjeantson, D. Birds. Cambridge Manuals in Archaeology (Cambridge University Press, 2009).
    Google Scholar 
    Lima-Ribeiro, M. S. et al. EcoClimate: a database of climate data from multiple models for past, present, and future for macroecologists and biogeographers. Biodivers. Inform. 10, 1–21 (2015).Article 

    Google Scholar 
    Varela, S., Lima-Ribeiro, M. S. & Terribile, L. C. A short guide to the climatic variables of the last glacial maximum for biogeographers. PLoS ONE 10, e0129037 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Elith, J. et al. Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29, 129–151 (2006).Article 

    Google Scholar 
    Elith, J., Leathwick, J. R. & Hastie, T. A working guide to boosted regression trees. J. Anim. Ecol. 77, 802–813 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Leathwick, J. R., Elith, J., Francis, M. P., Hastie, T. & Taylor, P. Variation in demersal fish species richness in the oceans surrounding New Zealand: an analysis using boosted regression trees. Mar. Ecol. Prog. Ser. 321, 267–281 (2006).Article 
    ADS 

    Google Scholar 
    Leathwick, J. R., Elith, J., Chadderton, W. L., Rowe, D. & Hastie, T. Dispersal, disturbance and the contrasting biogeographies of New Zealand’s diadromous and non-diadromous fish species. J. Biogeogr. 35, 1481–1497 (2008).Article 

    Google Scholar 
    Therneau, T. & Atkinson, B. Rpart: Recursive Partitioning and Regression Trees. R package version 4.1-15. https://CRAN.R-project.org/package=rpart (2019).Kuhn, M. Caret: Classification and Regression Training. R package version 6.0-88. https://CRAN.R-project.org/package=caret (2021). More

  • in

    The network nature of language endangerment hotspots

    Database utilizedThe database comprises information obtained with permission from the Catalogue of Endangered Languages that is hosted on the Endangered Languages Project platform (https://www.endangeredlanguages.com/). The Endangered Languages Project was first developed and launched by Google, and is currently overseen by First People’s Cultural Council and the Institute for Language Information and Technology at Eastern Michigan University. Information about the languages in this project is provided by the Catalogue, which is produced by the University of Hawai’i at Mānoa and Eastern Michigan University, with funding provided by the U.S. National Science Foundation (Grants #1058096 and #1057725) and the Luce Foundation. The project is supported by a team of global experts comprising its Governance Council and Advisory Committee.In general, the Catalogue aims to present all languages that communities and scholars have pointed out to be at some level of risk as well as languages that have become dormant. In addition to being the largest database of endangered languages globally, the Catalogue is updated periodically based on feedback gathered from language communities and scholars worldwide. The data therefore represents what was most accurately known about the state of each language’s vitality at its point of utilization. At the time of usage, there were 3423 languages represented in the Catalogue that were determined to be at various levels of risk. Assessment of each language’s risk level is carried out using the Language Endangerment Index, which was developed for the Catalogue’s purposes. The Index is used to assess the level of endangerment of any given language based on whether there is intergenerational transmission of the language (whether the language is being passed on to younger generations), its absolute number of speakers, speaker number trends (whether numbers are stable, increasing, or decreasing), and domains of language use (whether the language is used in a wide number of domains or limited ones). The levels of endangerment that the Index generates include ‘safe’, ‘vulnerable’, ‘threatened’, ‘endangered’, ‘severely endangered’, and ‘critically endangered’. Languages for which it remains unclear if the language has gone extinct or whose last fluent speaker is reported to have died in recent times are referred to as ‘dormant’. Given that the focus of the Catalogue is languages that are at some level of threat, safe languages are excluded in general. Where locality information is available, each language is also accompanied with its latitudinal and longitudinal coordinates.Steps taken to prepare the data for network analysisThe data obtained from the Catalogue was further organized and cleaned up for analysis.

    1.

    Identifier code
    Where available, the ISO 639-3 code for each language was utilized as its unique identifier. Otherwise, its LINGUIST List local use code was utilized. These are temporary codes that are not in the current version of the ISO 639-3 Standard for languages. For languages with neither, unique 3-letter codes were constructed.

    2.

    Endangerment level
    Each language’s endangerment level appeared together with a level of certainty score in the same cell in the original data file. Both pieces of information were split into separate columns and only endangerment levels were utilized.
    For languages where different data were available in the Catalogue depending on resource utilized, the data was listed in additional columns. The endangerment level data points utilized in these cases were the ones with the most complete and updated information. If there was no data available regarding endangerment level, this information was also reflected.

    3.

    Coordinates
    Where exact coordinates were not available, coordinates were approximated using Google maps based on the location description provided in the Catalogue source (e.g., the Tel Aviv district), attained from other sources such as Glottolog, UNESCO Atlas of the World’s Languages in Danger, or approximated from maps provided in other sources. ‘NA’ was indicated in the field for coordinates if none could be found.
    Coordinates found to be inaccurate were rejected, for example in the instance that coordinates provided indicate a different location than the country the language is supposedly found in. The above steps were then taken to populate the coordinates field.
    In instances where a language appears in more than one country, these are listed in separate rows as separate entries. Where there are two sets of coordinates for a country, the set that best corresponds with the written description in the Catalogue source, has greater detail, or is more recent is chosen. Where there are more than two sets of coordinates, a middle point is chosen as being representative of the language’s location, by plotting all coordinates on MapCustomizer (www.mapcustomizer.com).

    4.

    Language family
    On the Catalogue, the information regarding language family may be multi-tiered. For example, Laghuu falls under the Lolo-Burmese branch of the Sino-Tibetan family. For this study, the broader family is utilized—in the case of Laghuu the label ‘Sino-Tibetan’ is used.
    Mixed languages, pidgins, and creoles have all been categorized as ‘contact languages’.
    Language isolates are listed as ‘isolates’.

    5.

    Region

    The Catalogue groups ‘Mexico, Central America, Caribbean’ together under region. Central America and Caribbean are listed as separate regions in this study, with Mexico falling under Central America.Network constructionA spatial network of endangered languages was constructed from the database. Each node represented an endangered language, and edges or links depicted the distance between the locations of the languages as specified in the database. A distance matrix containing the distances between all endangered languages was computed by using functions from the ‘geosphere’ R package. Specifically, Haversine distances were computed for each pair of longitude and latitude points in the dataset. The radius of the earth used in the Haversine distance calculation is 6,378,137 m (for more details see: https://www.rdocumentation.org/packages/geosphere/versions/1.5-14/topics/distHaversine). Haversine distance refers to the shortest distance between two points on a spherical earth, also referred to as the “great-circle-distance”29.Sensitivity analyses of edge thresholdsThe distance matrix is a fully connected network with weighted, undirected links. We set out to capture the strongest or “closest” spatial relationships among the endangered languages, therefore an edge threshold was applied to the distance matrix such that only the edges in the xth lowest percentile were retained in the spatial network. Such an approach allows for the analysis of the most meaningful (i.e., the physically closest) spatial relations in the dataset and how they relate to language endangerment status. The edges were then transformed into unweighted connections to create a simple unweighted, undirected graph for analysis. In order to determine the value of x (i.e., the percentile at which the edge threshold is to be applied), we constructed 10 spatial networks that retained edges with distances below the 1st, 2nd, 3rd… 10th percentile (in increments of 1%) of all distances in the matrix. Additional information of the distances depicted by the edges in each of the 10 networks is provided in Supplementary Information.These 10 networks were then analyzed for their macro- and meso-scale network properties. A summary of macro and meso-scale network measures used in this analysis and their definitions is provided in Table 1, which depicts the 10 networks showing similar patterns in their network structures.Table 1 An overview of macro- and meso-level network measures of spatial networks with different thresholds.Full size tableResultsAs expected, network density and average degree of the networks, which serve as indicators of the number of edges relative to the number of nodes in the network, increased as the edge threshold used to connect nodes became more liberal. The relatively high values of C (i.e., high levels of local clustering among nodes) and low values of ASPL (i.e., relatively short paths despite large size of network) suggested the presence of small world structure30. The community detection analysis using the Louvain method31 indicated strong evidence of community structure in the networks—suggesting the presence of clusters of endangered languages.The point at which the vast majority of nodes was located within the largest connected component of the network occurred at the 5% edge threshold. Because the 5% network was not too fragmented, we report the analyses conducted on the largest connected component of the 5% network in the following subsections. Please see Supplementary Information for additional details behind the rationale for selecting the 5% network for further analyses. The smaller connected components were excluded. Note however that our results are robust across spatial networks of various edge thresholds (due to lack of space, please see Supplementary Information for a complete summary of all reported analyses conducted on all 10 spatial networks).Macro-level analysis: assortative mixing of endangerment statusesMethodTo investigate the macro-level structure of the spatial network of endangered languages, we computed the assortativity coefficient of the spatial network. Specifically, we wanted to know if the endangerment statuses of the languages tended to cluster at the global level of the entire network. If the assortativity coefficient is positive, the languages in the network would tend to be connected to languages of similar levels of endangerment. If the assortativity coefficient is negative, the languages in the network would tend to be connected to languages of dissimilar levels of endangerment.ResultsThere is a significant positive correlation (Spearman’s rank correlation) between the endangerment status of connected pairs of endangered languages in the network, r = 0.20, p  More

  • in

    Detailed analysis of habitat suitability curves for macroinvertebrates and functional feeding groups

    Poff, N. L. et al. The natural flow regime: A new paradigm for riverine conservation and restoration. Bioscience 47, 769–784 (1997).Article 

    Google Scholar 
    Bunn, S. E. & Arthington, A. H. Basic principles and ecological consequences of altered flow regimes for aquatic biodiversity. Environ. Manage. 30(4), 492–507 (2002).PubMed 
    Article 

    Google Scholar 
    Olden, J. D. et al. Are large-scale flow experiments informing the science and management of freshwater ecosystems?. Front. Ecol. Environ. 12, 176–185 (2014).Article 

    Google Scholar 
    Poff, N. L. Beyond the natural flow regime? Broadening the hydro-ecological foundation to meet environmental flows challenges in a non-stationary world. Freshw. Biol. 63, 1011–1021 (2018).Article 

    Google Scholar 
    Acreman, M. Ethical aspects of water and ecosystems. Water Policy 3, 257–265 (2001).Article 

    Google Scholar 
    Olden, J. D. & Naiman, R. J. Incorporating thermal regimes into environmental flows assessments: Modifying dam operations to restore freshwater ecosystem integrity. Freshw. Biol. 55, 86–107 (2010).Article 

    Google Scholar 
    Poff, N. L. & Zimmerman, J. K. H. Ecological responses to altered flow regimes: A literature review to inform the science and management of environmental flow. Freshw. Biol. 55, 194–205 (2010).Article 

    Google Scholar 
    Richter, B. D. & Thomas, G. A. Restoring environmental flows by modifying dam operations. Ecol. Soc. 12(1), 12 (2007).Article 

    Google Scholar 
    Tharme, R. E. A global perspective on environmental flow assessment: emerging trends in the development and application of environmental flow methodologies for rivers. River Res. Appl. 19, 397–441 (2003).Article 

    Google Scholar 
    Vӧrӧsmarty, C. J. et al. Global threats to human water security and river biodiversity. Nature 468, 334–334 (2010).Article 

    Google Scholar 
    Acreman, M. C. & Ferguson, A. J. D. Environmental flows and the European water framework directive. Freshw. Biol. 55, 32–48 (2010).Article 

    Google Scholar 
    Poff, N. L. & Matthews, J. H. Environmental flows in the Anthropocence: Past progress and future prospects. Curr. Opin. Environ. Sustain. 5, 667–675 (2003).Article 

    Google Scholar 
    Theodoropoulos, C. & Skoulikidis, N. Environmental flows: The European approach through the Water Framework Directive 2000/60/EC. In Proceedings of the 10th International Congress of the Hellenic Geographical Society 1140–1152 (2015).The Brisbane Declaration. Environmental flows are essential for freshwater ecosystem health and human well-being. In Declaration of the 10th International River Symposium 3–6 (Brisbane, Australia, 2007).Arthington, A. H. et al. The brisbane declaration and global action agenda on environmental flows. Front. Environ. Sci. 6, 45 (2018).Article 

    Google Scholar 
    European Commission. Ecological flows in the implementation of the Water Framework Directive. WFD CIS Guidance Document No. 31 (2015).Hirzel, A. H. & Le Lay, G. Habitat suitability modelling and niche theory. J. Appl. Ecol. 45, 1372–1381 (2008).Article 

    Google Scholar 
    Soberon, J. Grinnellian and Eltonian niches and geographic distributions of species. Ecol. Lett. 10(12), 1115–1123 (2007).PubMed 
    Article 

    Google Scholar 
    Ahmadi-Nedushan, B. et al. A review on statistical methods for the evaluation of the aquatic habitat suitability for instream flow assessment. River Res. Applic. 22, 503–523 (2006).Article 

    Google Scholar 
    Dolédec, S., Lamouroux, N., Fuchs, U. & Mérigoux, S. Modelling the hydraulic preferences of benthic macroinvertebrates in small European stream. Freshw. Biol. 52, 145–164 (2007).Article 

    Google Scholar 
    Katopodis, C. Case studies of instream flow modelling for fish habitat in Canadian Prairie Rivers. Can. Water Resour. J. 28, 199–216 (2003).Article 

    Google Scholar 
    Parasiewicz, P. Application of MesoHABSIM and target fish community approaches to restoration of the Quinebaug River, Connecticut and Massachusetts, U.S.A. River. Res. Appl. 24, 459–471 (2008).Article 

    Google Scholar 
    Piniweski, M. et al. Estimation of environmental flows in semi-natural lowland rivers – the Narew basin case study. Pol. J. Environ. Stud. 20(5), 1281–1293 (2011).
    Google Scholar 
    Theodoropoulos, C., Vourka, A., Skoulikidis, N., Rutschmann, P. & Stamou, A. Evaluating the performance of habitat models for predicting the environmental flow requirements of benthic macroinvertebrates. J. Ecohydraul. 3(1), 30–44 (2018).Article 

    Google Scholar 
    Yi, Y. et al. Evaluating the ecological influence of hydraulic projects: A review of aquatic habitat suitability models. Renew. Sustain. Energy Rev. 68, 748–762 (2017).Article 

    Google Scholar 
    Theodoropoulos, C., Skoulikidis, N., Rutschmann, P. & Stamou, A. Ecosystem-based environmental flow assessment in a Greek regulated river with the use of 2D hydrodynamic habitat modelling. River Res. Appl. 34(6), 538–547 (2018).Article 

    Google Scholar 
    Huryn, A. D. & Wallace, J. B. Life history and production of stream insects. Annu. Rev. Entomol. 45(1), 83–110 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wallace, J. B. & Webster, J. R. The role of macroinvertebrates in stream ecosystem function. Annu. Rev. Entomol. 41, 115–139 (1996).CAS 
    PubMed 
    Article 

    Google Scholar 
    Cummins, K. W. Structure and function of stream ecosystems. Bioscience 24, 631–641 (1974).Article 

    Google Scholar 
    Covich, A. P., Palmer, M. A. & Crowl, T. A. The role of benthic invertebrates species in freshwater ecosystems. Bioscience 49(2), 119–127 (1999).Article 

    Google Scholar 
    Dolédec, S., Statzner, B. & Bournaud, M. Species traits for future biomonitoring across ecoregions: Patterns along a human-impacted river. Freshw. Biol. 42, 737–758 (1999).Article 

    Google Scholar 
    Marzin, N. et al. Ecological assessment of running waters: Do macrophytes, macroinvertebrates, diatoms and fish show similar responses to human pressures?. Ecol. Ind. 23, 56–65 (2012).CAS 
    Article 

    Google Scholar 
    Statzner, B., Bady, P., Dolédec, S. & Schöll, F. Invertebrate traits for the biomonitoring of large European rivers: An initial assessment of trait patterns in least impacted river reaches. Freshw. Biol. 50, 2136–2161 (2005).Article 

    Google Scholar 
    Jowett, I. G. Hydraulic constraints on habitat suitability for benthic invertebrates in gravel-bed rivers. River Res. Appl. 19, 495–507 (2003).Article 

    Google Scholar 
    Dewson, Z. S., James, A. B. W. & Death, R. G. A review of the consequences of decreased flow for instream habitat and macroinvertebrates. J. North Am. Benthol. Soc. 26, 401–415 (2007).Article 

    Google Scholar 
    Wood, P. J. & Armitage, P. D. Biological effects of fine sediment in the lotic environment. Environ. Manage. 21(2), 203–217 (1997).CAS 
    PubMed 
    Article 

    Google Scholar 
    Rolls, R. J., Leigh, C. & Sheldon, F. Mechanistic effects of low-flow hydrology on riverine ecosystems: Ecological principles and consequences of alteration. Freshw. Sci. 31, 1163–1186 (2012).Article 

    Google Scholar 
    Graeber, D., Pusch, M. T., Lorenz, S. & Brauns, M. Cascading effects of flow reduction on the benthic invertebrate community in a lowland river. Hydrobiologia 717, 147–159 (2013).CAS 
    Article 

    Google Scholar 
    González, J. M., Recuerda, M. & Elosegi, A. Crowded waters: short-term response of invertebrate drift to water abstraction. Hydrobiologia 819, 39–51 (2018).Article 

    Google Scholar 
    Jowett, I. G., Richardson, J., Biggs, B. J. F., Hickey, C. W. & Quinn, J. M. Microhabitat preferences of benthic invertebrates and the development of generalised Deleatidium spp habitat suitability curves, applied to four New Zealand rivers. N. Z. J. Mar. Freshw. Res. 25(2), 187–199 (1991).Article 

    Google Scholar 
    Lamouroux, N. et al. The generality of abundance-environment relationships in microhabitats: A comment on Lancaster and Downes (2009). River Res. Appl. 26, 915–920 (2010).Article 

    Google Scholar 
    Mérigoux, S. & Dolédec, S. Hydraulic requirements of stream communities: A case study on invertebrates. Freshw. Biol. 49, 600–613 (2004).Article 

    Google Scholar 
    Lancaster, J. & Downes, B. J. Linking the hydraulic world of individual organisms to ecological processes: Putting ecology into ecohydraulics. River Res. Appl. 26, 385–403 (2009).Article 

    Google Scholar 
    Lancaster, J. & Hildrew, A. G. Flow refugia and the microdistribution of lotic macroinvertebrates. J. N. Am. Benthol. Soc. 12(4), 385–393 (1993).Article 

    Google Scholar 
    Chen, W. & Olden, J. D. Evaluating transferability of flow–ecology relationships across space, time and taxonomy. Freshw. Biol. 63, 817–830 (2017).Article 

    Google Scholar 
    Li, F., Cai, Q., Fu, X. & Liu, J. Construction of habitat suitability models (HSMs) for benthic macroinvertebrate and their applications to instream environmental flows: A case study in Xiangxi River of Three Gorges Reservior region China. Prog. Nat. Sci. 19, 359–367 (2009).Article 

    Google Scholar 
    Growns, I. O. & Davis, J. A. Longitudinal changes in near-bed flows and macroinvertebrate communities in a western Australian stream. J. North Am. Benthol. Soc. 13, 417–438 (1994).Article 

    Google Scholar 
    Shearer, K. A., Hayes, J. W., Jowett, I. G. & Olsen, D. A. Habitat suitability curves for benthic macroinvertebrates from a small New Zealand river. N. Z. J. Mar. Freshw. Res. 49, 178–191 (2015).Article 

    Google Scholar 
    Bovee, K. D. et al. Stream Habitat Analysis using the Instream Flow Incremental Methodology. USGS Inf. Technol. Rep. 1998–0004, 1–130 (1998).
    Google Scholar 
    Conallin, J., Boegh, E. & Jensen, J. K. Instream physical habitat modelling types: An analysis as stream hydromorphological modelling tools for EU water resource managers. Int. J. River Basin Manag. 8, 93–107 (2010).Article 

    Google Scholar 
    Poff, N. L., Tharme, R. E. & Arthington, A. H. Evolution of environmental flows assessment science, principles, and methodologies. In Water for the Environment: Policy, Science, and Integrated Management (eds Horne, A. et al.) 203–236 (Elsevier Press, Amsterdam, 2017).Chapter 

    Google Scholar 
    Bovee, K.D. Development and evaluation of habitat suitability criteria for use in the instream flow incremental methodology. Washington (DC): USDI Fish and Wildlife Service. Instream Flow Information Paper #21 FWS/OBS-86/7.Geological Survey, Biological Resources Division, Mid-Continent Ecological Science Centre, Fort Collins, Colorado (1986).Vismara, R., Azzellino, A., Bosi, R., Crosa, G. & Gentili, G. Preference curves for brown trout (Salmo trutta fario L.) in the River Adda, Northern Italy: comparing univariate and multivariate approaches. Regul. River 17, 37–50 (2001).Article 

    Google Scholar 
    Nestler, J. M., Milhous, R. T., Payne, T. R. & Smith, D. L. History and review of the habitat suitability criteria curve in applied aquatic ecology. River Res. Appl. 35, 1155–1180 (2019).Article 

    Google Scholar 
    Theodoropoulos, C., Skoulikidis, N., Stamou, A. & Dimitriou, E. Spatiotemporal variation in benthic-invertebrates-based physical Habitat modelling: Can we use generic instead of local and season-specific habitat suitability criteria?. Water 10, 1508 (2018).Article 

    Google Scholar 
    Gąbka, M., Jakubas, E., Janiak, T. & Golski, J. Rzeki Wełna i Flinta – charakterystyka obiektów badań, ich położenie i granice zlewni. In Koncepcja lasu Modelowego w Zarządzaniu i Ochronie Różnorodności Biologicznej rzek Wełny i Flinty(Wielkopolska (eds Batora, J. et al.) 21–30 (Bogucki Wydawnictwo Naukowe, Poznań, 2014).
    Google Scholar 
    Bartkowski, T. Rozwój polodowcowej sieci hydrograficznej w Wielkopolsce Środkowej (Zeszyty Naukowe UAM 8, 1957).Paluch, J. Wpływ działalności spółek wodnych istniejących w XIX i na początku wieku XX na terenie zlewni rzeki Wełny na stan jej hydrografii i stosunków wodnych. In Proceedings of the conference “Ecological problems of the Vełna River basin – status and directions of measures 2–26 (Wągrowiec, 2009).Jakubas, E. et al. Ocena stanu ekologicznego i zmian hydromorfologicznych rzek Wełny i Flinty. In Koncepcja lasu Modelowego w Zarządzaniu i Ochronie Różnorodności Biologicznej rzek Wełny i Flinty (Wielkopolska) (eds Batora, J. et al.) 141–150 (Bogucki Wydawnictwo Naukowe, Poznań, 2014).
    Google Scholar 
    Szoszkiewicz, K. et al. Podręcznik oceny wód płynących w oparciu o Hydromorfologiczny Indeks Rzeczny (Inspekcja Ochrony Środowiska, Biblioteka Monitoringu Środowiska, 2017).Emery, J. C. et al. Classifying the hydraulic performance of riffle–pool bedforms for habitat assessment and river rehabilitation design. River Res. Appl. 19, 533–549 (2003).Article 

    Google Scholar 
    Mueller, M., Pander, J. & Geist, J. Taxonomic sufficiency in freshwater ecosystems: Effects of taxonomic resolution, functional traits, and data transformation. Freshw. Sci. 32(3), 762–778 (2013).Article 

    Google Scholar 
    Schmidt-Kloiber, A., Graf, W., Lorenz, A. & Moog, O. The AQEM/STAR taxalist – a pan-European macro-invertebrate ecological database and taxa inventory. Hydrobiologia 566, 325–342 (2006).Article 

    Google Scholar 
    Clarke, K. R. & Warwick, R. M. Changes in Marine Communities: An Approach to Statistical Analysis and Interpretation 2nd edn. (Plymout, PRIMER-E (Plymouth Marine Laboratory, 2001).
    Google Scholar 
    Vimos-Lojano, D., Hampel, H., Vázquez, R. F. & Martínez-Capel, F. Community structure and functional feeding groups of macroinvertebrates in pristine Andean streams under different vegetation cover. Ecohydrol. Hydrobiol. 20(3), 357–368 (2020).Article 

    Google Scholar 
    Clarke, K. & Gorley, R. PRIMER v6: User Manual/Tutorial (Plymouth Marine Laboratory, Plymouth, 2006).
    Google Scholar 
    R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (https://www.R-project.org/, 2020)Oksanen, F. J., et al. Vegan: Community Ecology Package. R package Version 2.4–3. (https://CRAN.R-project.org/package=vegan, 2017)Jowett, I.G., Hayes, J.W. & Duncan, M.J. A guide to instream habitat survey methods and analysis. NIWA Science and Technology Series No. 54 (2008).Manly, B. F. J., McDonald, L. L. & Thomas, D. L. Resource Selection by Animals (Chapman and Hall, London, 1993).Book 

    Google Scholar 
    Bis, B. & Mikulec, A. Przewodnik do oceny stanu ekologicznego rzek na podstawie makrobezkręgowców bentosowych (Biblioteka Monitoringu Środowiska, 2013).Grygoruk, M. et al. Revealing the influence of hyporheic water exchange on the composition and abundance of bottom-dwelling macroinvertebrates in a temperate lowland river. Knowl. Manag. Aquat. Ecosyst. 442, 37. https://doi.org/10.1051/kmae/2021036 (2021).Article 

    Google Scholar 
    Degani, G. et al. Relationships between current velocity, depth and the invertebrate community in a stable river system. Hydrobiologia 263, 163–172 (1993).Article 

    Google Scholar 
    Lamberti, G. A., Entrekin, S. A., Griffiths, N. & Tiegs, S. Coarse Particulate Organic Matter: Storage, Transport, and Retention. In Methods Ecosystem Function Vol. 2 (eds Lamberti, G. A. & Hauer, F. R.) 55–69 (Elsevier Academic Press, Amsterdam, 2017).
    Google Scholar 
    Bell, N., Riis, T., Suren, A. M. & Baattrup-Pedersen, A. Distribution of invertebrates within beds of two morphologically contrasting stream macrophyte species. Fundam. Appl. Limnol. 183(4), 309–321 (2013).Article 

    Google Scholar 
    Wolters, J., Verdonschot, R. C. M., Schoelynck, J., Verdonschot, P. F. M. & Meire, P. The role of macrophyte structural complexity and water flow velocity in determining the epiphytic macroinvertebrate community composition in a lowland stream. Hydrobiologia 806, 157–173 (2018).CAS 
    Article 

    Google Scholar 
    Gore, J. A. & Nestler, J. M. Instream flow studies in perspective. Regul. Rivers Res. Manage. 2, 93–101 (1988).Article 

    Google Scholar 
    Hudson, H. R., Byrom, A. E. & Chadderton, W. L. A Critique of IFIM —Instream Habitat Simulation in the New Zealand Context (Department of Conservation, 2003).Stamou, A. et al. Determination of environmental flows in rivers using an integrated hydrological-hydrodynamic-habitat modelling approach. J. Environ. Manage. 209, 273–285 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wright, J. F., Blackburn, J. H., Clarke, R. T. & Furse, M. T. Macroinvertebrate-habitat associations in lowland rivers and their relevance to conservations. Int. Ver. Theor. Angew. Limnol. Verh. 25, 1515–1518 (1994).
    Google Scholar 
    Leszczyńska, J., Głowacki, Ł & Grzybkowska, M. Factors shaping species richness and biodiversity of riverine macroinvertebrate assemblages at the local and regional scale. Community Ecol. 18(3), 227–236 (2017).Article 

    Google Scholar 
    Gore, J. A., Crawford, D. J. & Addison, D. S. An analysis of artificial riffles and enhancement of benthic community diversity by Physical Habitat Simulation (PHABSIM) and direct observation. Regul. Rivers Res. Manage. 14(1), 69–77 (1998).Article 

    Google Scholar 
    Anderson, N. H. & Sedell, J. R. Detritus processing by macroinvertebrates in stream ecosystems. Ann. Rev. Entomol. 24, 351–377 (1979).Article 

    Google Scholar 
    Dunbar, M. J. et al. River discharge and local-scale physical habitat influence macroinvertebrate LIFE scores. Freshw. Biol. 55, 226–242 (2010).Article 

    Google Scholar 
    Acreman, M. et al. Environmental flows for natural, hybrid, and novel riverine ecosystems in a changing world. Front. Ecol. Environ. 12(8), 466–473 (2014).Article 

    Google Scholar 
    Jourdan, J. et al. Effects of changing climate on European stream invertebrate communities: a long-term data analysis. Sci. Total Environ. 621, 588–599 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Sarremejane, R. et al. Climate-driven hydrological variability determines inter-annual changes in stream invertebrate community assembly. Oikos 127, 1586–1595 (2018).Article 

    Google Scholar 
    Floury, M., Usseglio-Polatera, P., Ferreol, M., Delattre, C. & Souchon, Y. Global climate change in large European rivers: Long-term effects on macroinvertebrate communities and potential local confounding factors. Glob. Change Biol. 19, 1085–1099 (2013).Article 

    Google Scholar 
    Domisch, S., Jähnig, S. C. & Haase, P. Climate-change winners and losers: Stream macroinvertebrates of a submontane region in Central Europe. Freshw. Biol. 56, 2009–2020 (2011).Article 

    Google Scholar  More

  • in

    Alterations in rumen microbiota via oral fiber administration during early life in dairy cows

    Animals and dietsThe animal experiments were conducted in accordance with the Guidelines for Animal Experiments and Act on Welfare and Management of Animals, Hokkaido University, and all experimental procedures were approved by the Animal Care and Use Committee of Hokkaido University. All animal experiments were carried out in accordance with ARRIVE guidelines. Twenty newborn female Holstein calves with an average birth weight of 37.1 ± 1.0 kg (mean ± standard error) were randomly allocated to either the control or treatment group at birth. All calves were housed individually in separate calf hutches containing sawdust bedding. Feeding and managing of animals until weaning at 50 d of age was performed as described previously17. After supplementing colostrum at birth, calves in both groups were fed 4 L of pasteurized whole milk (44.2% crude protein [CP] and 29.3% fat on a dry matter [DM] basis) as a transition milk during the first week since birth. From 8 days until weaning at 50 days of age, milk replacer (28.0% CP and 18.0% fat on a DM basis) was fed twice daily at 0830 and 1600 h. Water, calf starter (22.9% CP, 11.0% neutral detergent fiber [NDF], 5.6% acid detergent fiber [ADF], 6.2% crude ash, and 3.0% ether extract on a DM basis), and chopped Timothy hay (3.4% CP, 53.1% NDF, 34.2% ADF, 4.3% crude ash, and 1.7% ether extract on a DM basis) were provided for ad libitum intake from 3 days of age. In addition to voluntary intake of solid diets, the calves in the treatment group were orally administered with a mixture of ground Timothy hay and psyllium (4.4% CP, 78.6% NDF, 5.8% ADF, 3.9% crude ash, and 0.3% ether extract on a DM basis) from 3 days until weaning at 50 days of age. Timothy hay was ground for oral administration using a Wiley grinder (WM-3, Irie Shokai) with a 2-mm screen. To improve the handling of the treatment diet for oral administration, we incorporated psyllium, which is a dietary fiber that primarily improves gastrointestinal conditions in humans and can be incorporated in oral electrolyte solution supplemented to neonatal calves38. As a treatment diet, ground Timothy hay (50 g) and psyllium (6 g) were mixed with 200 mL of water. Owing to the adhesiveness of psyllium, the treatment diet formed a “hay ball” and showed slight stickiness, which facilitates swallowing by calves. At 3–7 days of age, one hay ball (50 g of fibrous diet) was orally administered after morning milk feeding. From 8 days of age to weaning, an additional hay ball was fed immediately after evening milk feeding (100 g fibrous diet per day).After weaning, animals in both dietary groups were merged into the same herd and managed on the same farm under identical conditions. From 9 months of age until calving, heifers were fed a ration containing Timothy hay, alfalfa hay, fescue hay, and concentrate. After calving, the cows were fed a diet for lactating cows, as described in Supplementary Table S8. Diets comprised a total mixed ration and were fed twice daily at 0900 and 1600 h. All animals had ad libitum access to water and mineral blocks throughout the experiment. Daily milk production for each cow was measured for the first 30 days of the lactation period and the average values for each dietary group on a weekly and monthly basis were calculated. Milk yield for four animals in each dietary group were not recorded due to health problems including mastitis and displaced abomasum symptoms after calving.In this study, all animals (n = 20) were maintained until 9 months of age, without severe problems. Owing to health problems, several animals were excluded from the experiment before parturition as follows: three animals (one in the control group and two in the treatment group) at 60 days before the expected calving date and one animal in the control group at 21 days before the expected calving date. One animal in the control group (15 days after calving) and two animals in the treatment group (calving day) were diagnosed with displaced abomasum symptoms and were excluded from further sampling. Owing to technical problems, samples were not collected from three animals aged 7 days in the treatment group and one animal aged 21 days in the control group. All other samples (n = 176) were obtained at the target sampling points.Sampling of rumen contentsRumen contents were collected orally using a stomach tube. The stomach tube and the sample collection flask were thoroughly cleaned using water between sample collections from individual animals; the first fraction of the sample was discarded to avoid contamination from the previous sample and saliva. All samples were collected at 4 h after morning feeding. Rumen contents were collected at 7, 21, 35, 49, and 56 days, and at 9 months of age, 60 and 21 days before the expected calving date, at calving day, and 21 days after calving. The pH was measured using a pH meter (pH meter F-51; Horiba, Kyoto, Japan) immediately after sampling. Samples were collected in a sterile 50 mL tube and immediately placed on ice, followed by storage at − 30 °C until use.Chemical analysisRumen contents (1.0 g) were centrifuged at 16,000×g at 4 °C for 5 min, and the supernatant was collected. The SCFA content was analyzed using a gas chromatograph (GC-14B; Shimadzu, Kyoto, Japan) as described previously39. In brief, the supernatant of the rumen contents was mixed with 25% meta-phosphoric acid at a 5:1 ratio, incubated overnight at 4 °C, and centrifuged at 10,000×g at 4 °C. The supernatant was then mixed with crotonic acid as an internal standard and injected into a gas chromatograph equipped with an ULBON HR-20 M fused silica capillary column (0.53 mm i.d. × 30 m length, 3.0 µm film; Shinwa, Kyoto, Japan) and a flame-ionization detector. d/l-lactic acid levels were measured using a commercial assay kit (Megazyme International Ireland, Wicklow, Ireland) according to the manufacturer’s instructions. NH3-N levels were measured via the phenol-hypochloride reaction method40 using a microplate reader at 660 nm (ARVO MX; Perkin Elmer, Yokohama, Japan).DNA extraction and rumen microbiota profiling via amplicon sequencingTotal DNA was extracted and purified using the repeated bead-beating plus column method41. Rumen contents (0.25 g) were homogenized using sterile glass beads (0.4 g; 0.3 g of 0.1 mm and 0.1 g of 0.5 mm) and cell lysis buffer (1 mL; 500 mM NaCl, 50 mM Tris–HCl [pH 8.0], 50 mM ethylenediaminetetraacetic acid (EDTA), and 4% sodium dodecyl sulfate). The lysates were then incubated at 70 °C for 15 min, and the supernatant was collected for further processing. Bead-beating and incubation steps were repeated once, and all supernatants were combined. Total DNA was precipitated using 10 M ammonium acetate and isopropanol, followed by purification using the QIAamp Fast DNA Stool Mini Kit (Qiagen, Hilden, Germany). The DNA concentration was quantified using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and adjusted with Tris–EDTA buffer to the appropriate concentration.For a comprehensive analysis of rumen bacterial communities, the MiSeq sequencing platform (Illumina, San Diego, CA, USA) was used. Total DNA obtained from the rumen contents was diluted to a final concentration of 5 ng/μL and subjected to PCR amplification of the V3-V4 regions of the 16S rRNA gene using the primer sets S-D-Bact-0341-b-S-17 (5′-CCTACGGGNGGCWGCAG-3′) and S-D-Bact-0785-a-A-21 (5′-GACTACHVGGGTATCTAATCC-3′)42. The PCR mixture consisted of 12.5 μL of 2× KAPA HiFi HotStart Ready Mix (Roche Sequencing, Basel, Switzerland), 0.1 μM of each primer, and 2.5 μL of DNA (5 ng/μL). PCR amplification was performed according to the following program described previously9: initial denaturation at 95 °C for 3 min; 25 cycles at 95 °C for 30 s, 55 °C for 30 s, and 72 °C for 30 s; and a final extension step at 72 °C for 5 min. Amplicons were purified using AMPure XP beads (Beckman-Coulter, Brea, CA, USA) and subjected to sequencing on the Illumina MiSeq platform (Illumina) using the MiSeq Reagent Kit v3 (2 × 300 paired-end). Data obtained from amplicon sequencing using the MiSeq platform were analyzed using QIIME2 version 2019.443. Paired reads were filtered, dereplicated, merged, and chimera-filtered using the q2-dada2 plugin44 to generate ASVs. Taxonomic classification of the ASVs was performed at the phylum, class, order, family, and genus levels using the SILVA 132 99% operational taxonomic units, full length, seven level taxonomy classifier (silva-132-99-nb-classifier.qza). Sequenced data were processed further and analyzed using R software version 3.6.245. ASV and taxonomy tables generated using QIIME2 were imported into R and merged with the sample metadata using the Phyloseq Bioconductor packages46. ASVs identified as Archaea, chloroplasts, and mitochondria were excluded. All samples were rarefied to a sampling depth of 16,805 reads, which was the smallest number of reads observed per sample in the filtered ASV table. Alpha diversity indices including Chao1, ACE, Shannon, and Simpson indices were calculated using the phyloseq function “estimate_richness”. PCoA was performed to determine differences in the microbial community structure based on the Bray–Curtis dissimilarity matrices at the genus level using the Phyloseq package. Venn diagrams were generated using ASVs showing mean relative sequence abundances of  > 0.1% in either the control or the treatment groups at each sampling point. The relative abundance of each bacterial taxon was calculated by dividing the number of reads assigned to each taxon by the total number of reads. Taxa with an average relative abundance  > 0.1% in  > 50% of samples in either the control or treatment group during at least one sampling point were used for the analysis. Hierarchical cluster analysis of bacterial genera determined via amplicon sequencing at 21 days after calving and the weekly and monthly average milk yield for the first 30 days of lactation period was performed using the distances calculated from Spearman’s correlation and average linkage clustering.Quantification of target bacterial species/groups using real-time PCRThe relative abundance of known ruminal bacterial species and groups, including the total bacteria, F. succinogenes, R. flavefaciens, Ruminococcus albus, Butyrivibrio spp., Prevotella spp., Selenomonas ruminantium, Megasphaera elsdenii, Treponema spp., Streptococcus bovis, Anaerovibrio lipolytica, and Ruminobacter amylophilus, was quantified using real-time PCR. Amplification was performed using a Light Cycler 480 system (Roche Applied Science, Mannheim, Germany) with a KAPA SYBR Fast qPCR Kit (Roche Sequencing, Basel, Switzerland) and the respective primer sets (Supplementary Table S9). The standards used for the real-time PCR were prepared as described previously47. Briefly, plasmid DNA containing the respective target bacterial 16S rRNA gene sequence was obtained by PCR cloning using the species/genus-specific or bacterial universal primer sets. The concentration of the plasmid was determined with a spectrometer. Copy number of each standard plasmid was calculated using the molecular weight of nucleic acid and the length (base pair) of the cloned standard plasmid. Ten-fold dilution series ranging from 1 to 108 copies were prepared for each target and run along with the samples. The respective genes were quantified using standard curves obtained from the amplification profile of the dilution series of the plasmid DNA standard (Supplementary Table S9). The PCR cycling conditions and reaction mixture were the same as those reported previously48. The relative abundance of each bacterial target was expressed as the proportion (%) of the abundance of the 16S rRNA genes of each bacterial target relative to that of the total bacteria.Statistical analysisAll data were sorted based on animal age into two sets, from 7 to 56 days of age and from 9 months of age to 21 days after calving, and analyzed separately. Data on fermentation parameters and bacterial abundance quantified via real-time PCR were analyzed using a repeated measures model using GraphPad Prism software version 9.1 (GraphPad Software, San Diego, CA, USA) with the fixed effects of dietary group, age, and diet × age interaction, and the random effect of animals within the groups. The Greenhouse–Geisser correction was used where sphericity was violated. If the P-value for the treatment effect was  More

  • in

    Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera)

    Lavelle, P. et al. Soil invertebrates and ecosystem services. Eur. J. Soil Biol. 42, S3–S15 (2006).Article 

    Google Scholar 
    André, H. M., Noti, M. I. & Lebrun, P. The soil fauna: The other last biotic frontier. Biodiv. Conserv. 3, 45–56 (1994).Article 

    Google Scholar 
    Decaëns, T. Macroecological patterns in soil communities. Glob. Ecol. Biogeogr. 19, 287–302 (2010).Article 

    Google Scholar 
    IPCC. Global Warming of 1.5 °C. Summary for Policymakers. (World Meteorological Organization, 2018).Cardinale, B. J. et al. Biodiversity loss and its impact on humanity. Nature 486, 59–67 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Kardol, P., Reynolds, W. N., Norby, R. J. & Classen, A. T. Climate change effects on soil microarthropod abundance and community structure. Appl. Soil Ecol. 47, 37–44 (2011).Article 

    Google Scholar 
    Kaspari, M., Clay, N. A., Lucas, J., Yanoviak, S. P. & Kay, A. Thermal adaptation generates a diversity of thermal limits in a rainforest ant community. Glob. Change Biol. 21, 1092–1102 (2015).Article 

    Google Scholar 
    Baird, D. J. & Hajibabaei, M. Biomonitoring 2.0: A new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol. Ecol. 21, 2039–2044 (2012).PubMed 
    Article 

    Google Scholar 
    Leray, M. & Knowlton, N. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. PNAS 112, 2076–2081 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Beng, K. C. et al. The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics. Sci. Rep. 6, 1–13. https://doi.org/10.1038/srep24965 (2016).CAS 
    Article 

    Google Scholar 
    Zhang, K. et al. Plant diversity accurately predicts insect diversity in two tropical landscapes. Mol. Ecol. 25, 4407–4419 (2016).PubMed 
    Article 

    Google Scholar 
    Hebert, P. D., Cywinska, A., Ball, S. L. & Dewaard, J. R. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270, 313–321 (2003).CAS 
    Article 

    Google Scholar 
    Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W. & Hebert, P. D. DNA barcodes distinguish species of tropical Lepidoptera. PNAS 103, 968–971 (2006).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ratnasingham, S. & Hebert, P. D. N. A DNA-based registry for all animal species: The Barcode Index Number (BIN) system. PLoS ONE 8, e66213. https://doi.org/10.1371/journal.pone.0066213 (2013).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135–1145 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Porter, T. M. & Hajibabaei, M. Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Mol. Ecol. 27, 313–338 (2018).PubMed 
    Article 

    Google Scholar 
    Tang, M. et al. High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods Ecol. Evol. 6, 1034–1043 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Arribas, P., Andújar, C., Hopkins, K., Shepherd, M. & Vogler, A. P. Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil. Methods Ecol. Evol. 7, 1071–1081 (2016).Article 

    Google Scholar 
    Arribas, P., Andújar, C., Salces-Castellano, A., Emerson, B. C. & Vogler, A. P. The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding. Mol. Ecol. 30, 48–61 (2021).PubMed 
    Article 

    Google Scholar 
    Oliverio, A. M., Gan, H., Wickings, K. & Fierer, N. A DNA metabarcoding approach to characterize soil arthropod communities. Soil Biol. Biochem. 125, 37–43 (2018).CAS 
    Article 

    Google Scholar 
    Zinger, L. et al. Body size determines soil community assembly in a tropical forest. Mol. Ecol. 28, 528–543 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    McGee, K. M., Porter, T. M., Wright, M. & Hajibabaei, M. Drivers of tropical soil invertebrate community composition and richness across tropical secondary forests using DNA metasystematics. Sci. Rep. 10, 18429. https://doi.org/10.1038/s41598-020-75452-4 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hajibabaei, M., Spall, J. L., Shokralla, S. & van Konynenburg, S. Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecol. 12, 28. https://doi.org/10.1186/1472-6785-12-28 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gibson, J. et al. Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. PNAS 111, 8007–8012 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lamb, P. D. et al. How quantitative is metabarcoding: A meta-analytical approach. Mol. Ecol. 28, 420–430 (2019).PubMed 
    Article 

    Google Scholar 
    Piñol, J., Senar, M. A. & Symondson, W. O. The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative. Mol. Ecol. 28, 407–419 (2019).PubMed 
    Article 

    Google Scholar 
    Creedy, T. J., Ng, W. S. & Vogler, A. P. Toward accurate species-level metabarcoding of arthropod communities from the tropical forest canopy. Ecol. Evol. 9, 3105–3116 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lach, L., Parr, C., Abbott, K. Ant Ecology (Oxford University Press, 2010).Palacios-Vargas, J. G. & Castaño-Meneses, G. Seasonality and community composition of springtails in Mexican forest. In Arthropods of Tropical Forests. Spatio-Temporal Dynamics and Resource Use in the Canopy (eds. Basset, Y. et al.) 159–169 (Cambridge University Press, 2003).Bignell, D. E. & Eggleton, P. Termites in ecosystems. In Termites: Evolution, Sociality, Symbiosis, Ecology (eds Abe, T., Bignell, D. E. & Higashi, M.) 363–387 (Kluwer Academic Publishers, 2000).Anderson-Teixeira, K. J. et al. CTFS-Forest GEO: A worldwide network monitoring forests in an era of global change. Glob. Change Biol. 21, 528–549 (2015).Article 

    Google Scholar 
    Lamarre, G. P. et al. Monitoring tropical insects in the 21st century. Adv. Ecol. Res. 62, 295–330 (2020).Article 

    Google Scholar 
    Basset, Y. et al. Enemy-free space and the distribution of ants, springtails and termites in the soil of one tropical rainforest. Eur. J. Soil Biol. 99, 103193. https://doi.org/10.1016/j.ejsobi.2020.103193 (2020).Article 

    Google Scholar 
    Agosti, D., Majer, J. D., Alonso, L. E. & Schultz, T. R. Ants. Standards Methods for Measuring and Monitoring Biodiversity (Smithsonian Institution Press, 2000).Bourguignon, T., Leponce, M. & Roisin, Y. Insights into the termite assemblage of a neotropical rainforest from the spatio-temporal distribution of flying alates. Insect. Conserv. Divers. 2, 153–162 (2009).Article 

    Google Scholar 
    Yu, D. W. et al. Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol. Evol. 3, 613–623 (2012).Article 

    Google Scholar 
    Gaston, K. J. & Lawton, J. H. Patterns in the distribution and abundance of insect populations. Nature 331, 709–712 (1988).Article 

    Google Scholar 
    Liu, M., Clarke, L. J., Baker, S. C., Jordan, G. J. & Burridge, C. P. A practical guide to DNA metabarcoding for entomological ecologists. Ecol. Entomol. 45, 373–385 (2019).Article 

    Google Scholar 
    Zinger, L. et al. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions. Mol. Ecol. 28, 1857–1862 (2019).PubMed 
    Article 

    Google Scholar 
    Ficetola, G. F. et al. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Mol. Ecol. Res. 15, 543–556 (2015).CAS 
    Article 

    Google Scholar 
    Porter, T. M. & Hajibabaei, M. Automated high throughput animal CO1 metabarcode classification. Sci. Rep. 8, 1–10. https://doi.org/10.1038/s41598-018-22505-4 (2018).CAS 
    Article 

    Google Scholar 
    Marquina, D., Esparza-Salas, R., Roslin, T. & Ronquist, F. Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches. Mol. Ecol. Res. 19, 1516–1530 (2019).CAS 
    Article 

    Google Scholar 
    Porter, T. M. et al. Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators. Sci. Rep. 9, 1–11. https://doi.org/10.1038/s41598-019-54532-0 (2019).CAS 
    Article 

    Google Scholar 
    Basset, Y. et al. Cross-continental comparisons of butterfly assemblages in tropical rainforests: Implications for biological monitoring. Insect. Conserv. Divers 6, 223–233 (2013).Article 

    Google Scholar 
    Ryder Wilkie, K. T., Mertl, A. L. & Traniello, J. F. A. Biodiversity below ground: Probing the subterranean ant fauna of Amazonia. Naturwissenschaften 94, 725–731 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    André, H. M., Ducarme, X. & Lebrun, P. Soil biodiversity: Myth, reality or conning?. Oikos 96, 3–24 (2002).Article 

    Google Scholar 
    Wilson, J. J. DNA barcodes for insects. In DNA Barcodes: Methods and Protocols (eds Kress, W. J. & Erickson, D. L.) 17–46 (Springer, 2012).Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).CAS 
    PubMed 

    Google Scholar 
    Gibson, J. F. et al. Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing. PLoS ONE 10, e0138432. https://doi.org/10.1371/journal.pone.0138432 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hajibabaei, M., Porter, T. M., Wright, M. & Rudar, J. COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLoS One 14, e0220953. https://doi.org/10.1371/journal.pone.0220953 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bush, A. et al. DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness. PNAS 117, 8539–8545 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Calderón-Sanou, I. et al. From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices?. J. Biogeogr. 47, 193–206 (2020).Article 

    Google Scholar 
    Schloss, P. D. Reintroducing mothur: 10 years later. Appl. Env. Microbiol. 86, e02343-19. https://doi.org/10.1128/AEM.02343-19 (2020).Article 

    Google Scholar 
    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Boyer, F. et al. Obitools: A unix-inspired software package for DNA metabarcoding. Mol. Ecol. Res. 16, 176–182 (2016).CAS 
    Article 

    Google Scholar 
    Ratnasingham, S. mBRAVE: The multiplex barcode research and visualization environment. Biodivers. Inf. Sci. Stand. 3, e37986. https://doi.org/10.3897/biss.3.37986 (2019).Article 

    Google Scholar 
    Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584. https://doi.org/10.7717/peerj.2584 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Edgar, R. C. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gaston, K. J. Rarity (Springer, 1994).Kaspari, M. Litter ant patchiness at the 1–m2 scale: Disturbance dynamics in three Neotropical forests. Oecologia 107, 265–273 (1996).PubMed 
    Article 

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

    Google Scholar 
    Foster, Z. S. L., Sharpton, T. J. & Grünwald, N. J. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput. Biol. 13, e1005404. https://doi.org/10.1371/journal.pcbi.1005404 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-3 (2018).Hyams, D. G. CurveExpert Professional. A Comprehensive Data Analysis Software System for Windows, Mac, and Linux. Version 1.2.2. www.curveexpert.net (2011). Accessed 1 Jan 2022.Deagle, B. E. et al. Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?. Mol. Ecol. 28, 391–406 (2019).PubMed 
    Article 

    Google Scholar 
    Ficetola, G. F. et al. An In Silico approach for the evaluation of DNA barcodes. BMC Genom. 11, 434. https://doi.org/10.1186/1471-2164-11-434 (2010).CAS 
    Article 

    Google Scholar 
    Auer, L., Mariadassou, M., O’Donohue, M., Klopp, C. & Hernandez-Raquet, G. Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description. Mol. Ecol. Res. 17, e122–e132. https://doi.org/10.1111/1755-0998.12700 (2017).CAS 
    Article 

    Google Scholar 
    Novotný, V. & Basset, Y. Rare species in communities of tropical insect herbivores: Pondering the mystery of singletons. Oikos 89, 564–572 (2000).Article 

    Google Scholar 
    Seifert, B. & Goropashnaya, A. V. Ideal phenotypes and mismatching haplotypes-errors of mtDNA treeing in ants (Hymenoptera: Formicidae) detected by standardized morphometry. Org. Divers. Evol. 4, 295–305 (2004).Article 

    Google Scholar 
    Gotzek, D., Clarke, J. & Shoemaker, D. Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae). BMC Evol. Biol. 10, 300. https://doi.org/10.1186/1471-2148-10-300 (2010).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Meza-Lázaro, R. N., Poteaux, C., Bayona-Vásquez, N. J., Branstetter, M. G. & Zaldívar-Riverón, A. Extensive mitochondrial heteroplasmy in the neotropical ants of the Ectatomma ruidum complex (Formicidae: Ectatomminae). Mit. DNA Part A 29, 1203–1214 (2018).Article 

    Google Scholar 
    Saitoh, S. et al. A quantitative protocol for DNA metabarcoding of springtails (Collembola). Genome 59, 705–723 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Elbrecht, V. et al. Validation of COI metabarcoding primers for terrestrial arthropods. PeerJ 7, e7745. https://doi.org/10.7717/peerj.7745 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Schenk, J., Geisen, S., Kleinbölting, N. & Traunspurger, W. Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth. Metabarcoding Metagenom. 3, e46704. https://doi.org/10.3897/mbmg.3.46704 (2019).Article 

    Google Scholar 
    Elbrecht, V. & Leese, F. Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass—Sequence relationships with an innovative metabarcoding protocol. PLoS One 10, e0130324. https://doi.org/10.1371/journal.pone.0130324 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bista, I. et al. Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples. Mol. Ecol. Res. 18, 1020–1034 (2018).CAS 
    Article 

    Google Scholar 
    Ji, Y. et al. SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes. Mol. Ecol. Res. 20, 256–267 (2020).CAS 
    Article 

    Google Scholar 
    Steiner, F. M. et al. Tetramorium tsushimae, a new invasive ant in North America. Biol. Invasions 8, 117–123 (2006).Article 

    Google Scholar 
    Wetterer, J. K. Worldwide spread of the penny ant, Tetramorium bicarinatum (Hymenoptera: Formicidae). Sociobiology 54, 811–830 (2009).
    Google Scholar 
    Roisin, Y. et al. Vertical stratification of the termite assemblage in a neotropical forest. Oecologia 149, 301–311 (2006).PubMed 
    Article 

    Google Scholar 
    Basset, Y. et al. Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites. Metabarcoding Metagenom. 4, 151–163. https://doi.org/10.3897/mbmg.4.58572 (2020).Article 

    Google Scholar  More

  • in

    Modelling of life cycle cost of conventional and alternative vehicles

    Life cycle cost modelAn analysis of life cycle costs is an economic analysis of the assessment of the total cost of acquisition, ownership and liquidation of a product. It is applicable during the entire life cycle of the product or a life cycle stage or combination of different stages21 and22.There are five period phases of the vehicle life cycle:Generally, the total costs for the above listed phases are acquisition costs, ownership costs and liquidation costs21 and22. For the LCC model, I recommend to divide the life cycle costs into four categories:$$LCC={C}_{P}+{C}_{M}+{C}_{O}+{C}_{D},$$
    (1)
    $${LCC}_{s}=frac{LCC}{t},$$
    (2)

    where LCC—the life cycle cost of vehicles, LCCs—the specific life cycle cost of vehicles, CP—the vehicle purchase cost, CM—the maintenance cost, CO—operating state of vehicle cost, CD—the vehicle disposal cost, t—the time of vehicle operation.The model for evaluating the economic viability of products is based on the general LCC model which is based on acquisition and ownership costs$$LCC={C}_{P}+{C}_{OW},$$
    (3)

    where CP—purchase cost, COW—ownership costs.Acquisition cost (CP) is represented by the purchase price at the time of acquisition of the assessed passenger vehicle.Ownership cost (COW) is significant during the life cycle of a motor vehicle and varies according to the type of the vehicle. This cost includes the costs of maintenance and operation time can be defined as follows10$${C}_{Ow}={C}_{M}+{C}_{O},$$
    (4)

    where CM—cost of maintenance, CO—operation cost.The cost of ownership a vehicle (COW) can be defined as follows$${C}_{OW}={C}_{O}+{C}_{MC}+{C}_{MP},$$
    (5)

    where CO—operation cost, CMC—corrective maintenance cost, CMP—preventive maintenance cost.The cost of ownership (COW) may include the operating and maintenance costs which consist of the corrective maintenance cost (CMC) and the cost of preventive maintenance (CMP) of a motor vehicle.Calculation of operating costsOperating cost CO is determined by the price and amount consumed of conventional or alternative types of fuel. It cover the cost of fuel CF, operating fluids, oils and lubricants COL that are supplied during vehicle operation (not during service inspection), tyres CT, accumulator batteries CAB, vehicle insurance fee and road tax or other mandatory fees CIRT, cost of the motorway tax sticker CMT, mandatory vehicle inspection and emission measurement in special vehicles CETC. The costs are calculated according to$${C}_{O}={C}_{F}+{C}_{OL}+{C}_{T}+{C}_{AB}+{C}_{IRT}+{C}_{MT}+{C}_{ETC}.$$
    (6)
    Fuel costs (CF) are affected by the average consumption of a given type of propulsion vehicle. Then the comparative fuel costs (CF) can be expressed by the equation$${C}_{F}=frac{{bar{c}}_{aF}}{100}{p}_{F}{t}_{l},$$
    (7)

    where CF—total fuel costs (EUR), (bar{c})aF—average fuel consumption (l/100 km), pF—fuel price (EUR/l), tl—service life of a passenger vehicle (km).Costs for operating fluids, oils and lubricants (COL) are any costs for operating fluids, oils and lubricants that are replenished during operation and not during service maintenance; it can be expressed by the equation$${C}_{OL}=frac{{bar{c}}_{aOL}}{100}{p}_{OL}{t}_{l},$$
    (8)

    where (bar{c})aOL—average consumption of oil and lubricant (l/100 km), pOL—price of oil and lubricant (EUR/l).The cost of tyres (CT) can be expressed by the equation$${C}_{T}=frac{{t}_{l}}{{bar{d}}_{aT}}{n}_{T}{p}_{T},$$
    (9)

    where (bar{d})aT—average life of a passenger vehicle tyre (km), nt—number of tyres on the passenger vehicle (pc), pT—price of one piece of tyre (EUR).Accumulator battery costs (CAB) —can be expressed by the equation$${C}_{AB}=frac{{t}_{l}}{{bar{d}}_{aAB}}{n}_{AB}{p}_{AB},$$
    (10)

    where (bar{d}_{aB})—average life of one accumulator battery (km), nAB—number of accumulator batteries in the passenger vehicle (pc), pAB—price of an accumulator battery (EUR).Costs arising from laws (CIRT) are the costs of motor vehicle insurance (compulsory liability, accident insurance, or other). Some of them can be omitted in case of the same costs due to the simplification of the model. Otherwise, they can be expressed by the equation$${C}_{IRT}=left({C}_{SI}+{C}_{AI}+{C}_{RT}+{C}_{R}right){t}_{la},$$
    (11)
    where CS1—price of mandatory annual insurance of a passenger vehicle (EUR), CA1—price of the annual accident insurance of a passenger vehicle (EUR), CRT—price of annual road tax (EUR), CR—price of statutory fee (EUR), tla—operating time of the passenger vehicle until decommissioning (years).The cost of obtaining a motorway sticker (CMT) may be omitted if the same type of passenger vehicle is compared. Otherwise, the cost of a motorway sticker (CMT) can be expressed by the equation$${C}_{MT}={c}_{MT}{t}_{la},$$
    (12)

    where cMT—price of annual motorway sticker for the passenger vehicle (EUR).The costs of the mandatory vehicle inspection and emission measurement (CETC) include the costs incurred for the measurement of emissions of the drive engine unit (CE) and for the technical inspection of the passenger vehicle (CTC). For the proposed model, the costs of the mandatory technical inspections and emission measurements can be expressed by the equation$${C}_{ETC}=left({C}_{E}+{C}_{TC}right)frac{{y}_{n}}{{t}_{la}},$$
    (13)

    where CE—costs related to the measurement of passenger vehicle emissions (EUR), CTC—costs of mandatory technical inspection (EUR), yn—number of years of legal validity of emission measurement and technical condition for the given type of the passenger vehicle (years).Calculation of maintenance costThe total costs for vehicle maintenance CM consist of the cost of preventive maintenance CMP and the cost of corrective maintenance CMC10,11$${C}_{M}={C}_{MC}+{C}_{MP}.$$
    (14)
    Vehicle maintenance costs include the cost of material and the cost of labour$${C}_{M}={(C}_{MCM}+{C}_{MCL}+{C}_{MCF})+left({C}_{MPM}+{C}_{MPL}+{C}_{MPF}right),$$
    (15)

    where CM—cumulative maintenance costs, CMC—corrective maintenance costs, CMP—preventive maintenance costs, CMCM—costs of material used for corrective maintenance, CMCL—costs of labour force for corrective maintenance, CMCF—costs of workshop equipment used for corrective maintenance, CMPM—costs of material used for preventive maintenance, CMPL—costs of labour force for preventive maintenance, CMPF—costs of workshop equipment used for preventive maintenance.

    Preventive maintenance costs (CMP) are costs that include all costs associated with preventive maintenance performed to reduce degradation and mitigate the likelihood of failure. At present, preventive maintenance is performed at predetermined time intervals (according to the manufacturer’s preventive maintenance program) or when a specified number of kilometres are not covered before the next service maintenance, depending on the time. In practice, for passenger cars, it is usually 1 or 2 years, depending on the use of engine oil. This mainly includes the cost of:

    material consumed during preventive maintenance,

    work spent on preventive maintenance,

    workshop equipment, training of preventive maintenance specialists.$${C}_{MP}=frac{{t}_{l}}{MTB{M}_{p}}left({C}_{MPM}+{(bar{c}}_{p}{bar{t}}_{pm})right),$$
    (17)

    where MTBMp—mean operating time between preventive maintenances (km), CMPM—costs of material used for preventive maintenance (EUR), (bar{c})p—average hourly cost of labour and workshop equipment used for maintenance (EUR/hour), ̅tpm—mean time of labour-intensity per one preventive maintenance (hour).

    Design of a model for the analysis of selected life cycle costs of a passenger motor vehicleThe model for performing an analysis of life cycle costs for the purchase of a new motor vehicle is based on the basic Eq. (3), (18). We will not count the costs of improvement (CE) and the costs of the decommissioning phase (CD) for the mentioned model due to the calculations of costs that are unnecessary for the analysis. Then the model can be expressed as follows$$LCC={C}_{P}+{C}_{O}+{C}_{M}.$$
    (18)
    Then, the following Eqs. (6), (7), (8), (9), (10), (11), (12), (13), (16) and (17) are substituted into the given equation, and the selected costs can be calculated for individual vehicles. The resulting model for calculating the LCC costs has the following form$$LCC={C}_{p}+frac{{bar{c}}_{aF}}{100}{p}_{F}{t}_{l}+frac{{bar{c}}_{aOL}}{100}{p}_{OL}{t}_{l}+frac{{t}_{l}}{{bar{d}}_{aT}}{n}_{T}{p}_{T}+frac{{t}_{l}}{{bar{d}}_{aAB}}{n}_{AB}{p}_{AB}+{C}_{SI}{t}_{la}+{c}_{MT}{t}_{la}+left({C}_{E}+{C}_{TC}right)frac{{y}_{n}}{{t}_{la}}+frac{{t}_{l}}{MTBF}left({bar{c}}_{m}+{(bar{c}}_{p}{bar{t}}_{pc})right)+frac{{t}_{l}}{MTB{M}_{p}}left({C}_{OMPM}+{bar{(c}}_{p}{bar{t}}_{pm})right).$$
    (19)
    It is presented in a Fig. 6.Figure 6Structure of model input parameters for LCC model calculation.Full size imageIn this way, the cumulative costs for each passenger motor vehicle are calculated. Since the passenger motor vehicles may have a different service life tl which is expressed in kilometres, it is recommended to convert this equation to specific costs which are related to one kilometre of use. The selected LCCS life cycle specific costs can be expressed by the following equation$${LCC}_{S}=frac{LCC}{{t}_{l}}.$$
    (20)
    LCC model input values and items affecting ownership costs for alternative drivesThe process of the calculation of selected life cycle costs for the propulsion of passenger vehicles and the structure of individual cost items is shown in Fig. 6. These are the input parameters to the LCC model.The total life cycle costs are divided into two main cost groups, which are the ownership and acquisition costs for a given drive type. Fuel costs are determined by the price and the quantity of conventional or alternative fuel consumed. For the calculation of the selected LCCs, the authors of the paper assume that the availability of conventional and alternative fuels is not limited in any way. It is assumed that the availability of fuels is ideal, which is not entirely true in practice. This is dependent on the support for each alternative fuel in each state.In practice, therefore, multiple costs may arise due to the distance to the refuelling station to provide alternative fuels such as E85, CNG, LPG and hydrogen. In addition, there is a distance to the charging station for electric drives.Another item that affects the cost of operation for hybrid passenger vehicles is the percentage of alternative fuel driving, which can have a significant impact on life cycle costs. Values for this item are given as a percentage, which is then converted into the number of kilometres driven on alternative and conventional fuel.One of the important parameters for calculating the life cycle operating costs for the hybrid-electric and electric drive is the setting of a threshold value for the capacity of the electric vehicle battery (EV battery) when the replacement is performed. For the model calculation, a limit value of 70% of the electric vehicle battery capacity at 20 °C was set.Return on investmentReturn on investment (ROI) is a performance measure used to evaluate the efficiency or profitability of an investment or compare the efficiency of a number of different investments. ROI tries to directly measure the amount of return on a particular investment, relative to the investment’s cost. To calculate ROI, the benefit (or return) of an investment is divided by the cost of the investment. The result is expressed as a percentage or a ratio12,23.For our calculation of the return on investment ROI on alternative and conventional passenger car propulsion the following formula is used, which is expressed as a percentage$$ROI=frac{{LCC}_{A}-{LCC}_{C}}{{LCC}_{C}}100,$$
    (21)

    where LCCA—selected live cycle costs of the alternative passenger car propulsion (EUR), LCCC—selected live cycle costs of the conventional passenger car propulsion (EUR).The return on investment of an alternative vehicle ROIAV purchase expresses after how many kilometres the increased cost of purchasing an alternative fuel vehicle compared to a conventional one is recovered. If the value is negative, the payback will not occur for various reasons. The following equation is used to calculate ROIAV$${ROI}_{AV}=frac{{C}_{{P}_{AV}}-{C}_{{P}_{CV}}}{frac{{C}_{O{W}_{CV}}-{C}_{O{W}_{AV}}}{{t}_{l}}}$$
    (22)

    where ({C}_{{P}_{AV}})—purchase cost on alternative vehicle (EUR), ({C}_{{P}_{CV}})—purchase cost on conventional vehicle (EUR), ({C}_{O{W}_{CV}})—ownership cost on conventional vehicle (EUR), ({C}_{O{W}_{AV}})—ownership cost on alternative vehicle (EUR), tl—service life of the passenger vehicle (km).Ownership costs on conventional vehicle are expressed by the following equation$${C}_{{OW}_{CV}}={left(frac{{bar{c}}_{aF}}{100}{p}_{F}{t}_{l}+frac{{bar{c}}_{aOL}}{100}{p}_{OL}{t}_{l}+frac{{t}_{l}}{{bar{d}}_{aT}}{n}_{T}{p}_{T}+frac{{t}_{l}}{{bar{d}}_{aAB}}{n}_{AB}{p}_{AB}+{C}_{SI}{t}_{la}+{c}_{MT}{t}_{la}+left({C}_{E}+{C}_{TC}right)frac{{y}_{n}}{{t}_{la}}+frac{{t}_{l}}{MTBF}left({bar{c}}_{m}+{(bar{c}}_{p}{bar{t}}_{pc})right)+frac{{t}_{l}}{MTB{M}_{p}}left({C}_{OMPM}+({bar{c}}_{p}{bar{t}}_{pm})right)right)}_{CV}.$$
    (23)
    Ownership costs on alternative vehicle are expressed by the following equation$${C}_{{OW}_{AV}}={left(frac{{bar{c}}_{aF}}{100}{p}_{F}{t}_{l}+frac{{bar{c}}_{aOL}}{100}{p}_{OL}{t}_{l}+frac{{t}_{l}}{{bar{d}}_{aT}}{n}_{T}{p}_{T}+frac{{t}_{l}}{{bar{d}}_{aAB}}{n}_{AB}{p}_{AB}+{C}_{SI}{t}_{la}+{c}_{MT}{t}_{la}+left({C}_{E}+{C}_{TC}right)frac{{y}_{n}}{{t}_{la}}+frac{{t}_{l}}{MTBF}left({bar{c}}_{m}+{(bar{c}}_{p}{bar{t}}_{pc})right)+frac{{t}_{l}}{MTB{M}_{p}}left({C}_{OMPM}+({bar{c}}_{p}{bar{t}}_{pm})right)right)}_{AV}.$$
    (24)
    The rate of return on investment for the purchase of an alternative vehicle depending on the kilometres travelled to is expressed by the following equation$${ROI}_{AV({t}_{o})}={(C}_{{P}_{AV}}-{C}_{{P}_{CV}})-({C}_{O{W}_{CV}left({t}_{o}right)}-{C}_{O{W}_{AV}left({t}_{o}right)}) quad text{when} ;to = (0-tl)$$
    (25)

    where to—operation of the passenger vehicle (km). More

  • in

    Bateman gradients from first principles

    Model 1: Evolution of multiple mating and mate monopolisation under ancestral monogamyIn all models, I assume a large population with a 1:1 sex ratio. I begin with what is possibly the simplest model set-up for deriving Bateman functions in a scenario that is completely symmetrical aside from gamete number. Assume a monogamous, externally fertilising population where parents pair up and release their gametes into a nest. That is, every individual in the initial population participates in exactly one fertilisation event (the equivalent of a mating). Now consider a mutant individual that can attract multiple mates of the opposite type to release gametes into its nest, with no competition from other individuals of its own type. This simple set-up avoids asymmetries arising from internal fertilisation, and the complication of direct gamete competition for the multiply mating mutant individual (which is examined in Models 2–3), placing focus directly on the core of the problem: the asymmetry arising in fertilisation from imbalanced gamete numbers. All gametes are released in one burst by all individuals, but the focal individual may achieve ‘multiple matings’ simply by monopolising multiple mates at its nest. The reproductive success of the focal individual is then equivalent to the number of fertilisations that take place in that nest. Our aim is to understand how the reproductive success of an individual deviating from the monogamous population strategy and instead mating with (hat{m}) individuals of the opposite type is altered. A strong positive relationship between (hat{m}) and reproductive success then indicates a steep Bateman gradient. If Bateman’s assertion is correct, the resulting gradient should be steeper for the type that produces the larger number of gametes. Note that there is a game-theoretical25 flavour to this setting, where the focus is on the fitness of a rare mutant in a population with a fixed resident strategy.The two types are labelled with x and y, which could correspond to the two sexes, depending on what gamete numbers are assigned to them. The number of gametes produced by a single individual is labelled nx and ny, and the total number of gametes in a nest (or more generally, a fertilisation arena which could be internal or external) is labelled with Nx and Ny. To compute the number of fertilisations in a nest with a total of Nx and Ny gametes, I use a fertilisation function first derived by Togashi et al.24 purely from biophysical principles, treating the two gamete types symmetrically, with no pre-existing assumptions about differences between females and males or their gametes (for a broader context and comparison to other functions, see Table 1 and function F7 in19). Any sex-specific differences arise only retrospectively after different gamete numbers are assigned to x and y of which either one could be male or female. The fertilisation function is (fleft({N}_{x},{N}_{y}right)={N}_{x}{N}_{y}frac{{e}^{a{N}_{x}}-{e}^{a{N}_{y}}}{{{N}_{x}e}^{a{N}_{x}}-{N}_{y}{e}^{a{N}_{y}}}), where a is a parameter controlling fertilisation efficiency (for the special case Nx = Ny the function is defined as (fleft({N}_{x},{N}_{y}right)=frac{a{N}_{x}^{2}}{1+a{N}_{x}})19,24, which is also the limit of f when Ny → Nx).In a monogamous resident pair, we have simply Nx = nx and Ny = ny. But if a mutant individual of type x is able to attract (hat{m}) fertilisation partners of type y, then for that individual ({N}_{y}=hat{m}{n}_{y}), and the corresponding Bateman function is$${b}_{x}left(hat{m}right)=fleft({N}_{x},{N}_{y}right)=fleft({n}_{x},hat{m}{n}_{y}right)$$
    (1)
    where the fertilisation function f is as described above. Because of symmetry, the corresponding function for y is found simply by swapping x and y. This function can reproduce the characteristic Bateman gradient asymmetry as gamete numbers diverge (progressing from isogamy to anisogamy in Fig. 1), showing how Bateman’s assertion follows from biophysical effects that arise from unequal numbers of fusing particles: the fertilisation function f is derived solely from such biophysical effects, not from any sex-specific assumptions. Equation (1) makes no reference to sexes, and they only become specified when values are assigned to nx and ny. For example, if nx = 10 and ny = 10,000, the female Bateman function is ({b}_{x}left(hat{m}right)) and the male Bateman function ({b}_{y}left(hat{m}right)), where for the latter all xs in Eq. (1) are replaced with ys and vice versa. The labels x and y are truly just labels. While there are inevitably assumptions built into the equations, crucially we can be certain there are no sex-specific assumptions. Yet the typical shapes reminiscent of Bateman gradients arise from the model when different values are specified for nx and ny (Fig. 1).Fig. 1: The Bateman function of Eq. (1).This figure shows how the basic Bateman gradient asymmetry arises from simple biophysics and mathematics of fertilisation. The population is monogamous aside from a mutant individual, whose number of fertilisation partners (‘matings’) varies on the horizontal axes within panels. a–d show the effect of variation in sex-specific gamete numbers under efficient fertilisation, while e–h show the effect of variation in sex-specific gamete numbers under inefficient fertilisation. Parameter values used are shown in the figure. Females (gamete number nx) are indicated by blue crosses and connecting lines, while males (gamete number ny) are indicated by black dots and connecting lines. Under isogamy, females and males are undefined, and the two colours overlap. The typical sex-specific shapes of Bateman gradients arise from a single equation (which itself is not sex-specific) when a difference in gamete numbers is assigned to nx and ny, confirming Bateman’s intuition that the primary cause of the difference in selection is that females produce fewer gametes than males. The entire range of gamete number ratios presented in the figure is observed in nature, from equal gamete size in many unicellular organisms39 to vertebrates, where sperm count per ejaculate can commonly exceed 109 (see ref. 40 and Supplementary Information therein).Full size imageGamete limitation changes the results quantitatively so that under conditions of poor fertilisation efficiency a larger imbalance in gamete numbers is needed for Bateman gradients to diverge to a similar extent. However, even under inefficient fertilisation, the Bateman gradients do not reverse.Model 2: An external fertiliser model with population-level polygamy and gamete competitionModel 1 presented the simplest possible scenario, where all individuals except a rare mutant mate only once, and gamete competition (sperm competition26, but without assigning either gamete type to be sperm) was thus excluded for the focal mutant individual. Now I generalise from this to a situation that remains entirely symmetrical, but where the resident number of matings can take on any value, and then derive the Bateman function for a rare mutant that deviates from this population-level value. This set-up allows for gamete competition for the focal mutant individual, a crucial addition because of the empirical and theoretical importance of sperm competition26, as well as earlier theory suggesting that polyandry decreases the sex difference in Bateman gradients2.The biological set-up is such that there is a large population and a large number of patches (fertilisation arenas) where multiple individuals of both sexes can release their gametes for fertilisation. After all individuals have released their gametes, those in each patch mix freely and fertilisations take place randomly. Set up in this way, the model is again identical from the perspective of both sexes, and gamete number can be isolated as the sole possible causal factor in any subsequent differences that may arise, extending from the initially monogamous and gamete competition-free scenario of Model 1. All individuals of both sexes are assumed to initially have the same strategy: to divide their nx or ny gametes equally between m patches, and distribute themselves in such a way that gametes from m individuals of each type release gametes into each patch (the number of individuals of each sex per patch need not necessarily be strictly equal to m, but this is the simplest assumption to account for the fact that gamete competition tends to increase with multiple ‘matings’). Now, if a rare x mutant divides its gametes evenly into (hat{m}) randomly selected patches, its gamete number per patch and consequently competitiveness in each patch is altered. Therefore, gametes of a mutant of type x will gain, on average, a fraction ({c}_{x}=left({n}_{x}/hat{m}right)/{N}_{x}) of the fertilisations in that patch, where ({N}_{x}={n}_{x}/hat{m}+(m-1){n}_{x}/m). To compute the number of realised fertilisations in a patch, I use the same fertilisation function as in Model 1, where the mutant number of gametes in a patch is Nx as above and the number of gametes of the opposite type is ({N}_{y}=mfrac{{n}_{y}}{m}={n}_{y}). All the components are now in place to write down the Bateman function corresponding to this scenario, for a mutant of type x:$${b}_{x}left(hat{m},mright)=hat{m}{c}_{x}fleft({N}_{x},{N}_{y}right)$$
    (2)
    where cx, Nx and Ny are as defined above, and the fertilisation function f is as in Model 1. For completeness, define bx(0, m) = 0, which is necessarily true, but useful to define separately because division by 0 renders Eq. (2) formally undefined when (hat{m}=0).As in Model 1, Eq. (2) makes no reference to sexes, and they only become specified when values are assigned to nx and ny (Fig. 2).Fig. 2: The Bateman function of Eq. (2) for an externally fertilising population with potential for population-wide polygamy and gamete competition.Results are shown for two values of resident matings (m = 1 and m = 2). a–h show the effect of variation in sex-specific gamete numbers and in fertilisation efficiency with m = 1, while i–p show the same with m = 2. Parameter values used are shown in the figure. The value m = 2 is used here because it is comparable to the mean number of matings in Bateman’s1 work (see Fig. 3 for corresponding results with internal fertilisation, but note that the aim of the models is not to quantitatively reproduce Bateman’s results). Females (gamete number nx) are indicated by blue crosses and connecting lines, while males (gamete number ny) are indicated by black dots and connecting lines. Under isogamy, females and males are undefined, and the two colours overlap. Further variation in m is examined in Fig. 4.Full size imageModel 3: An internal fertiliser modelModels 1–2 were set up with the central aim of full symmetry and exclusion of any sex-specific assumptions. Internal fertilisation breaks this symmetry by introducing a sex-specific assumption other than gamete number. Bateman gradients are, however, most commonly applied to situations with internal fertilisation where females are gamete recipients and males are gamete donors27. I therefore construct a model accounting for internal fertilisation. Where Eqs. (1) and (2) allowed no sex differences aside from gamete number, here I additionally consider the fact that females receive gametes while males donate them.As in model 2, there is a very large population, and I assume that in the resident population, all females and males mate exactly m times. It is then considered how a rare mutant individual’s (of either sex) fitness depends on its number of matings (hat{m}).I use the same fertilisation function as in Models 1-2. Consider first the female perspective (labelled with x). A female produces nx gametes and retains them internally. Each female mates with m males, who also mate with m females, dividing their gametes evenly over these matings. Therefore a mutant female receives (hat{m}frac{{n}_{y}}{m}) male gametes, and her reproductive success is$${b}_{x}left(hat{m},mright)=fleft({n}_{x},hat{m}frac{{n}_{y}}{m}right)$$
    (3)
    A mutant male, on the other hand, mates with (hat{m}) females, each of which mates with m−1 additional males. Therefore, the mutant male’s mating partners will receive a total of ({{N}_{y}=n}_{y}/hat{m}+(m-1){n}_{y}/{m}) male gametes. Thus, the mutant male gains a fraction ({c}_{y}=left({n}_{y}/hat{m}right)/{N}_{y}) of the fertilisations with each female, while the total reproductive success per female is f(nx,Ny). The mutant male’s reproductive success is therefore$${b}_{y}left(hat{m},mright)=hat{m}{c}_{y}fleft({n}_{x},{N}_{y}right)$$
    (4)
    To avoid division by 0, we can again define by (0, m) = 0, analogous to Model 2. In contrast to Models 1–2, there are now separate equations for each sex because of the additional sex-specific assumption of internal fertilisation, but no further sex-specific assumptions are used in their derivation. Visually the Bateman functions (Fig. 3) are nevertheless very similar to Model 2, and again reproduce the sex-specific shapes first proposed by Bateman1 when fertilisation is efficient. However, an interesting exception arises when relatively weak asymmetry in gamete numbers is combined with inefficient fertilisation and gamete limitation. When these conditions are combined with internal fertilisation, Bateman gradients can theoretically be reversed.Fig. 3: The Bateman functions of Eqs. (3) and (4) for internal fertilisation.Where Figs. 1 and 2 show that the sex-specific shapes of Bateman functions are ultimately caused by differences in gamete number, Fig. 3 shows that internal fertilisation does not invalidate this outcome when fertilisation is efficient. As in Fig. 2, results are shown for two values of resident matings (1 and 2), and the value m = 2 is used because it is comparable to the mean number of matings in Bateman’s1 work. a–h show the effect of variation in sex-specific gamete numbers and in fertilisation efficiency with m = 1, while i–p show the same with m = 2. Parameter values used are shown in the figure. Inefficient fertilisation combined with relatively low asymmetry in gamete numbers and the added asymmetry of internal fertilisation can in principle reverse the Bateman gradients (second and fourth row). Females (gamete number nx) are indicated by blue crosses and connecting lines, while males (gamete number ny) are indicated by black dots and connecting lines.Full size image More

  • in

    Spatio-temporal evolution characteristics analysis and optimization prediction of urban green infrastructure: a case study of Beijing, China

    Birenboim, A. The influence of urban environments on our subjective momentary experiences. Environ. Plan. B-Urban Anal. CIty Sci. 45, 915–932. https://doi.org/10.1177/2399808317690149 (2018).Article 

    Google Scholar 
    Flores, A., Pickett, S. T. A., Zipperer, W. C., Pouyat, R. V. & Pirani, R. Adopting a modern ecological view of the metropolitan landscape: The case of a greenspace system for the New York City region. Landsc. Urban Plan. 39, 295–308. https://doi.org/10.1016/S0169-2046(97)00084-4 (1998).Article 

    Google Scholar 
    Weijs-Perrée, M., Dane, G., Berg, P. V. D. & Dorst, M. V. A multi-level path analysis of the relationships between the momentary experience characteristics, satisfaction with urban public spaces, and momentary- and long-term subjective wellbeing. Int. J. Environ. Res. Public Health. https://doi.org/10.3390/ijerph16193621 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Paulin, M. J. et al. Application of the natural capital model to assess changes in ecosystem services from changes in green infrastructure in Amsterdam. Ecosyst. Serv. 43, 101114. https://doi.org/10.1016/j.ecoser.2020.101114 (2020).Article 

    Google Scholar 
    Derkzen, M. L., van Teeffelen, A. J. A., Verburg, P. H. & Diamond, S. Quantifying urban ecosystem services based on high-resolution data of urban green space: An assessment for Rotterdam, the Netherlands. J. Appl. Ecol. 52, 1020–1032. https://doi.org/10.1111/1365-2664.12469 (2015).Article 

    Google Scholar 
    Leiva, M. A., Santibanez, D. A., Ibarra, S., Matus, P. & Seguel, R. A five-year study of particulate matter (PM2.5) and cerebrovascular diseases. Environ. Pollut. 181, 1–6. https://doi.org/10.1016/j.envpol.2013.05.057 (2013).CAS 
    Article 

    Google Scholar 
    Venkataramanan, V. et al. Knowledge, attitudes, intentions, and behavior related to green infrastructure for flood management: A systematic literature review. Sci. Total Environ. 720, 137606. https://doi.org/10.1016/j.scitotenv.2020.137606 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Wang, G. Z., Han, Q. & De Vries, B. The multi-objective spatial optimization of urban land use based on low-carbon city planning. Ecol. Indic. 125, 107540. https://doi.org/10.1016/j.ecolind.2021.107540 (2021).CAS 
    Article 

    Google Scholar 
    Cameron, R. W. F. et al. The domestic garden—Its contribution to urban green infrastructure. Urban For. Urban Green. 11, 129–137. https://doi.org/10.1016/j.ufug.2012.01.002 (2012).Article 

    Google Scholar 
    De la Sota, C., Ruffato-Ferreira, V. J., Ruiz-Garcia, L. & Alvarez, S. Urban green infrastructure as a strategy of climate change mitigation. A case study in northern Spain. Urban For. Urban Green. 40, 145–151. https://doi.org/10.1016/j.ufug.2018.09.004 (2019).Article 

    Google Scholar 
    Pongsakorn, S., Jiang, X. R. & Sullivan, W. C. Green infrastructure, green stormwater infrastructure, and human health a review. Curr. Landscape. Ecol. Rep. 2, 96–110. https://doi.org/10.1007/s40823-017-0028-y (2017).Article 

    Google Scholar 
    Liu, O. Y. & Russo, A. Assessing the contribution of urban green spaces in green infrastructure strategy planning for urban ecosystem conditions and services (Sust. Cities Soc., 2021). https://doi.org/10.1016/j.scs.2021.102772.Book 

    Google Scholar 
    McMahon, E. T. Green infrastructure. Plan. Commission. J. (2000).Mell, I. C. Green Infrastructure Concepts, Perceptions and Its Use in Spatial Planning. Doctor of Philosophy Thesis (Planning and Landscape Newcastle University, 2010).
    Google Scholar 
    Wang, J. X. & Banzhaf, E. Towards a better understanding of green infrastructure: A critical review. Ecol. Indic. 85, 758–772. https://doi.org/10.1016/j.ecolind.2017.09.018 (2018).Article 

    Google Scholar 
    Young, R., Zanders, J., Lieberknecht, K. & Fassman-Beck, E. A comprehensive typology for mainstreaming urban green infrastructure. J. Hydrol. 519, 2571–2583. https://doi.org/10.1016/j.jhydrol.2014.05.048 (2014).Article 

    Google Scholar 
    Wang, J. X., Xu, C., Pauleit, S., Kindler, A. & Banzhaf, E. Spatial patterns of urban green infrastructure for equity: A novel exploration. J. Clean Prod. 238, 117858. https://doi.org/10.1016/j.jclepro.2019.117858 (2019).Article 

    Google Scholar 
    Cook, E. A. Landscape structure indices for assessing urban ecological networks. Landsc. Urban Plan. 58, 269–280 (2002).Article 

    Google Scholar 
    Vogt, P. & Riitters, K. GuidosToolbox: Universal digital image object analysis. Eur. J. Remote Sens. 50, 352–361. https://doi.org/10.1080/22797254.2017.1330650 (2017).Article 

    Google Scholar 
    Vogt, P., Riitters, K. H., Estreguil, C., Kozak, J. & Wade, T. G. Mapping spatial patterns with morphological image processing. Landsc. Ecol. 22, 171–177. https://doi.org/10.1007/s10980-006-9013-2 (2007).Article 

    Google Scholar 
    Kuttner, M., Hainz-Renetzeder, C., Hermann, A. & Wrbka, T. Borders without barriers—Structural functionality and green infrastructure in the Austrian-Hungarian transboundary region of Lake Neusiedl. Ecol. Indic. 31, 59–72. https://doi.org/10.1016/j.ecolind.2012.04.014 (2013).Article 

    Google Scholar 
    Ma, Q. W., Li, Y. H. & Xu, L. H. Identification of green infrastructure networks based on ecosystem services in a rapidly urbanizing area. J. Clean Prod. 300, 126945. https://doi.org/10.1016/j.jclepro.2021.126945 (2021).Article 

    Google Scholar 
    Furberg, D., Ban, Y. & Mörtberg, U. Monitoring urban green infrastructure changes and impact on habitat connectivity using high-resolution satellite data. Remote Sens. 12, 3072. https://doi.org/10.3390/rs12183072 (2020).Article 

    Google Scholar 
    Barbati, A., Corona, P., Salvati, L. & Gasparella, L. Natural forest expansion into suburban countryside: Gained ground for a green infrastructure?. Urban For. Urban Green. 12, 36–43. https://doi.org/10.1016/j.ufug.2012.11 (2013).Article 

    Google Scholar 
    Fluhrer, T., Chapa, F. & Hack, J. A methodology for assessing the implementation potential for retrofitted and multifunctional urban green infrastructure in public areas of the global south. Sustainability https://doi.org/10.3390/su13010384 (2021).Article 

    Google Scholar 
    Carroll, C., McRae, B. H. & Brookes, A. Use of linkage mapping and centrality analysis across habitat gradients to conserve connectivity of gray wolf populations in western North America. Conserv. Biol. 26, 78–87. https://doi.org/10.1111/j.1523-1739.2011.01753.x (2012).Article 
    PubMed 

    Google Scholar 
    Saura, S. & Torne, J. Conefor Sensinode 2.2: A software package for quantifying the importance of habitat patches for landscape connectivity. Environ. Modell. Softw. 24, 135–139 (2009).Article 

    Google Scholar 
    Jaworek-Jakubska, J., Filipiak, M., Michalski, A. & Napierała-Filipiak, A. Spatio-temporal changes of urban forests and planning evolution in a highly dynamical urban area: The case study of Wrocław, Poland. Forests 11, 17. https://doi.org/10.3390/f11010017 (2019).Article 

    Google Scholar 
    Ren, Z. B., He, X. Y., Zheng, H. F. & Wei, H. X. Spatio-temporal patterns of urban forest basal area under China’s rapid urban expansion and greening: Implications for urban green infrastructure management. Forests 9, 272. https://doi.org/10.3390/f9050272 (2018).Article 

    Google Scholar 
    Elliott, R. M. et al. Identifying linkages between urban green infrastructure and ecosystem services using an expert opinion methodology. Ambio 49, 569–583. https://doi.org/10.1007/s13280-019-01223-9 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    García, A. M., Santé, I., Loureiro, X. & Miranda, D. Green infrastructure spatial planning considering ecosystem services assessment and trade-off analysis. Application at landscape scale in Galicia region (NW Spain). Ecosyst. Serv. 43, 101115. https://doi.org/10.1016/j.ecoser.2020.101115 (2020).Article 

    Google Scholar 
    Tiwari, A. & Kumar, P. Integrated dispersion-deposition modelling for air pollutant reduction via green infrastructure at an urban scale. Sci. Total Environ. 723, 138078. https://doi.org/10.1016/j.scitotenv.2020.138078 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Zhang, Y. Q. et al. Unexpected air quality impacts from implementation of green infrastructure in urban environments: A Kansas City case study. Sci. Total Environ. 744, 140960. https://doi.org/10.1016/j.scitotenv.2020.140960 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Alizadehtazi, B., Gurian, P. L. & Montalto, F. A. Observed variability in soil moisture in engineered urban green infrastructure systems and linkages to ecosystem services. J. Hydrol. 590, 125381. https://doi.org/10.1016/j.jhydrol.2020.125381 (2020).Article 

    Google Scholar 
    Dennis, M., Cook, P. A., James, P., Wheater, C. P. & Lindley, S. J. Relationships between health outcomes in older populations and urban green infrastructure size, quality and proximity. BMC Public Health https://doi.org/10.1186/s12889-020-08762-x (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Van Oijstaeijen, W., Van Passel, S. & Cools, J. Urban green infrastructure: A review on valuation toolkits from an urban planning perspective. J. Environ. Manag. 267, 110603. https://doi.org/10.1016/j.jenvman.2020.110603 (2020).Article 

    Google Scholar 
    Majekodunmi, M., Emmanuel, R. & Jafry, T. A spatial exploration of deprivation and green infrastructure ecosystem services within Glasgow city. Urban For. Urban Green. 52, 126698. https://doi.org/10.1016/j.ufug.2020.126698 (2020).Article 

    Google Scholar 
    Liberalesso, T., Oliveira Cruz, C., Matos Silva, C. & Manso, M. Green infrastructure and public policies: An international review of green roofs and green walls incentives. Land Use Pol. 96, 104693. https://doi.org/10.1016/j.landusepol.2020.104693 (2020).Article 

    Google Scholar 
    Lin, H. Y., Qian, J., Yan, L. J. & Huang, S. R. Analysis of spatial-temporal pattern and scenario simulation of green infrastructure in Wuyi County based on morphological spatial pattern analysis and CA-Markov model. Acta Agricult. Zhejiangensis. https://doi.org/10.3969/j.issn.1004-1524.2019.07.21 (2019).Article 

    Google Scholar 
    Mitsova, D., Shuster, W. & Wang, X. H. A cellular automata model of land cover change to integrate urban growth with open space conservation. Landsc. Urban Plan. 99, 141–153. https://doi.org/10.1016/j.landurbplan.2010.10.001 (2011).Article 

    Google Scholar 
    Dennis, M. et al. Mapping urban green infrastructure: A novel landscape-based approach to incorporating land use and land cover in the mapping of human-dominated systems. Land 7, 17. https://doi.org/10.3390/land7010017 (2018).Article 

    Google Scholar 
    Hu, Y. J. et al. Urban expansion and farmland loss in Beijing during 1980–2015. Sustainability 10, 3927. https://doi.org/10.3390/su10113927 (2018).Article 

    Google Scholar 
    Li, W. J., Wang, Y., Xie, S. Y., Sun, R. H. & Cheng, X. Impacts of landscape multifunctionality change on landscape ecological risk in a megacity, China: A case study of Beijing. Ecol. Indic. 117 (2020).Song, W., Pijanowski, B. C. & Tayyebi, A. Urban expansion and its consumption of high-quality farmland in Beijing, China. Ecol. Indic. 54, 60–70. https://doi.org/10.1016/j.ecolind.2015.02.015 (2015).Article 

    Google Scholar 
    Li, Z. Z., Cheng, X. Q. & Han, H. R. Future impacts of land use change on ecosystem services under different scenarios in the ecological conservation area, Beijing, China. Forests https://doi.org/10.3390/f11050584 (2020).Article 

    Google Scholar 
    Liu, D. Y. et al. Interoperable scenario simulation of land-use policy for Beijing-Tianjin-Hebei region, China. Land Use Pol. 75, 155–165. https://doi.org/10.1016/j.landusepol.2018.03.040 (2018).Article 

    Google Scholar 
    Mo, W. B., Wang, Y., Zhang, Y. X. & Zhuang, D. F. Impacts of road network expansion on landscape ecological risk in a megacity, China: A case study of Beijing. Sci. Total Environ. 574, 1000–1011. https://doi.org/10.1016/j.scitotenv.2016.09.048 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Melgani, F. & Bruzzone, L. Classification of hyperspectral remote sensing images with support vector machines. IEEE Trans. Geosci. Remote Sens. 42, 1778–1790. https://doi.org/10.1109/Tgrs.2004.831865 (2004).Article 

    Google Scholar 
    Zhang, C., Wang, T. J., Atkinson, P. M., Pan, X. & Li, H. P. A novel multi-parameter support vector machine for image classification. Int. J. Remote Sens. 36, 1890–1906. https://doi.org/10.1080/01431161.2015.1029096 (2015).CAS 
    Article 

    Google Scholar 
    Peterson, L. K., Bergen, K. M., Brown, D. G., Vashchuk, L. & Blam, Y. Forested land-cover patterns and trends over changing forest management eras in the Siberian Baikal region. For. Ecol. Manag. 257, 911–922. https://doi.org/10.1016/j.foreco.2008.10.037 (2009).Article 

    Google Scholar 
    Sang, L. L., Zhang, C., Yang, J. Y., Zhu, D. H. & Yun, W. J. Simulation of land use spatial pattern of towns and villages based on CA-Markov model. Math. Comput. Model. 54, 938–943. https://doi.org/10.1016/j.mcm.2010.11.019 (2011).Article 

    Google Scholar 
    Liu, D. Y., Zheng, X. Q. & Wang, H. B. Land-use Simulation and Decision-Support system (LandSDS): Seamlessly integrating system dynamics, agent-based model, and cellular automata. Ecol. Model. 417, 108924. https://doi.org/10.1016/j.ecolmodel.2019.108924 (2020).Article 

    Google Scholar 
    Kazak, J. K. The use of a decision support system for sustainable urbanization and thermal comfort in adaptation to climate change actions-The case of the Wroclaw larger urban zone (Poland). Sustainability https://doi.org/10.3390/su10041083 (2013).Article 

    Google Scholar 
    Sonnenberg, F. A. & Beck, J. R. Markov-models in medical decision-making—A practical guide. Med. Decis. Mak. 13, 322–338. https://doi.org/10.1177/0272989×9301300409 (1993).CAS 
    Article 

    Google Scholar 
    Nadoushan, M. A., Soffianian, A. & Alebrahim, A. Modeling land use/cover changes by the combination of Markov chain and cellular automata Markov CA-Markov models. Int. J. Environ. Health Res. https://doi.org/10.4103/WKMP-0092.159922 (2015).Article 

    Google Scholar 
    Mansour, S., Al-Belushi, M. & Al-Awadhi, T. Monitoring land use and land cover changes in the mountainous cities of Oman using GIS and CA-Markov modelling techniques. Land Use Pol. 91, 104414. https://doi.org/10.1016/j.landusepol.2019.104414 (2020).Article 

    Google Scholar 
    Karimi, H., Jafarnezhad, J., Khaledi, J. & Ahmadi, P. Monitoring and prediction of land use/land cover changes using CA-Markov model: A case study of Ravansar County in Iran. Arab. J. Geosci. https://doi.org/10.1007/s12517-018-3940-5 (2018).Article 

    Google Scholar 
    Mondal, M. S., Sharma, N. C. P. K. G. & Kappas, M. Statistical independence test and validation of CA Markov land use land cover (LULC) prediction results. Egypt. J. Remote Sens. Space Sci. https://doi.org/10.1016/j.ejrs.2016.08.001 (2016).Article 

    Google Scholar 
    Liu, Q. et al. Multi-scenario simulation of land use change and its eco-environmental effect in Hainan Island based on CA-Markov model. Ecol. Environ. Sci. 30, 1522–1531. https://doi.org/10.16258/j.cnki.1674-5906.2021.07.021 (2021).Article 

    Google Scholar 
    Pontius, R. G. Statistical methods to partition effects of quantity and location during comparison of categorical maps at multiple resolutions. Photogramm. Eng. Remote Sens. 68, 1041–1049 (2002).
    Google Scholar 
    Soille, P. & Vogt, P. Morphological segmentation of binary patterns. Pattern Recognit. Lett. 30, 456–459 (2009).Article 

    Google Scholar 
    Chang, Q., Liu, X. W., Wu, J. S. & He, P. MSPA-based urban green infrastructure planning and management approach for urban sustainability: Case study of Longgang in China. J. Urban Plan. Dev. https://doi.org/10.1061/(asce)up.1943-5444.0000247 (2015).Article 

    Google Scholar 
    Li, K. M. et al. Spatiotemporal evolution characteristics of urban green infrastructure in central Liaoning urban agglomeration during the past 20 years based on landscape ecology and morphology. Acta Ecol. Sin. https://doi.org/10.5846/stxb202007221918 (2021).Article 

    Google Scholar 
    Ning, J. et al. Spatiotemporal patterns and characteristics of land-use change in China during 2010–2015. J. Geogr. Sci. 28, 547–562. https://doi.org/10.1007/s11442-018-1490-0 (2018).Article 

    Google Scholar 
    Sawyer, S. C., Epps, C. W. & Brashares, J. S. Placing linkages among fragmented habitats: Do least-cost models reflect how animals use landscapes?. J. Appl. Ecol. 48, 668–678. https://doi.org/10.1111/j.1365-2664.2011.01970.x (2011).Article 

    Google Scholar 
    Yin, G. Y., Liu, L. M. & Jiang, X. L. The sustainable arable land use pattern under the tradeoff of agricultural production, economic development, and ecological protection—An analysis of Dongting Lake basin, China. Environ. Sci. Pollut. Res. 24, 25329–25345. https://doi.org/10.1007/s11356-017-0132-x (2017).Article 

    Google Scholar  More