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    The relationship between ecosystem services and human modification displays decoupling across global delta systems

    Cumming, G. S. et al. Implications of agricultural transitions and urbanization for ecosystem services. Nature 515, 50–57 (2014).CAS 
    Article 

    Google Scholar 
    Cumming, G. S. & Von Cramon-Taubadel, S. Linking economic growth pathways and environmental sustainability by understanding development as alternate social-ecological regimes. Proc. Natl. Acad. Sci.115, 9533–9538 (2018).CAS 
    Article 

    Google Scholar 
    Costanza, R. et al. The value of the world’s ecosystem services and natural capital. Nature 387, 253–260 (1997).CAS 
    Article 

    Google Scholar 
    de Groot, R. S., Alkemade, R., Braat, L., Hein, L. & Willemen, L. Challenges in integrating the concept of ecosystem services and values in landscape planning, management and decision making. Ecol. Complex. 7, 260–272 (2010).Article 

    Google Scholar 
    Clapp, J. Financialization, distance and global food politics. J. Peasant Stud. 41, 797–814 (2014).Article 

    Google Scholar 
    Crona, B. I. et al. Masked, diluted and drowned out: how global seafood trade weakens signals from marine ecosystems. Fish Fish. 17, 1175–1182 (2016).Article 

    Google Scholar 
    United Nations Environment Programme International Resource Panel. Decoupling Natural Resource Use and Environmental Impacts from Economic Growth (2011).Srinivasana, U. T. et al. The debt of nations and the distribution of ecological impacts from human activities. Proc. Natl. Acad. Sci. 105, 1768–1773 (2008).Article 

    Google Scholar 
    Rist, L. et al. Applying resilience thinking to production ecosystems. Ecosphere 5, 1–11 (2014).Article 

    Google Scholar 
    Dermody, B. J. et al. A virtual water network of the Roman world. Hydrol. Earth Syst. Sci. 18, 5025–5040 (2014).Article 

    Google Scholar 
    Maskell, L. C. et al. Exploring the ecological constraints to multiple ecosystem service delivery and biodiversity. J. Appl. Ecol. 50, 561–571 (2013).Article 

    Google Scholar 
    Potschin, M. B. & Haines-Young, R. H. Ecosystem services: Exploring a geographical perspective. Prog. Phys. Geogr. 35, 575–594 (2011).Article 

    Google Scholar 
    Peng, J. et al. Ecosystem services response to urbanization in metropolitan areas: Thresholds identification. Sci. Total Environ. 607–608, 706–714 (2017).Article 
    CAS 

    Google Scholar 
    Millennium Ecosystem Assessment. Ecosystems and human well-being: Biodiversity synthesis (2005). https://doi.org/10.1057/9780230625600Díaz, S. et al. Assessing nature’s contributions to people: Recognizing culture, and diverse sources of knowledge, can improve assessments. Science 359, 270–272 (2018).Article 

    Google Scholar 
    Wallace, K. J. Classification of ecosystem services: Problems and solutions. Biol. Conserv. 139, 235–246 (2007).Article 

    Google Scholar 
    Lee, H. & Lautenbach, S. A quantitative review of relationships between ecosystem services. Ecol. Indic. 66, 340–351 (2016).Article 

    Google Scholar 
    Bennett, E. M., Peterson, G. D. & Gordon, L. J. Understanding relationships among multiple ecosystem services. Ecol. Lett. 12, 1394–1404 (2009).Article 

    Google Scholar 
    Saidi, N. & Spray, C. Ecosystem services bundles: Challenges and opportunities for implementation and further research. Environ. Res. Lett. 13, 113001 (2018).Cord, A. F. et al. Towards systematic analyses of ecosystem service trade-offs and synergies: Main concepts, methods and the road ahead. Ecosyst. Serv. 28, 264–272 (2017).Article 

    Google Scholar 
    Mitsch, W. J. & Gosselink, J. G. The value of wetlands: importance of scale and landscape setting. Ecol. Econ. 35, 25–33 (2000).Article 

    Google Scholar 
    Raudsepp-Hearne, C., Peterson, G. D. & Bennett, E. M. Ecosystem service bundles for analyzing tradeoffs in diverse landscapes. Proc. Natl. Acad. Sci. 107, 5242–5247 (2010).CAS 
    Article 

    Google Scholar 
    Hamann, M., Biggs, R. & Reyers, B. Mapping social-ecological systems: Identifying ‘green-loop’ and ‘red-loop’ dynamics based on characteristic bundles of ecosystem service use. Glob. Environ. Change 34, 218–226 (2015).Article 

    Google Scholar 
    Macklin, M. G. & Lewin, J. The rivers of civilization. Quat. Sci. Rev. 114, 228–244 (2015).Article 

    Google Scholar 
    Barbier, E. B. et al. The value of estuarine and coastal ecosystem services. Ecol. Monogr. 81, 169–193 (2011).Article 

    Google Scholar 
    Stanley, D. J. & Warne, A. G. Sea level and initiation of Predynastic culture in the Nile delta. Nature 363, 435–438 (1993).Article 

    Google Scholar 
    Costanza, R. et al. Changes in the global value of ecosystem services. Glob. Environ. Change 26, 152–158 (2014).Article 

    Google Scholar 
    Edmonds, D. A., Caldwell, R. L., Brondizio, E. S. & Siani, S. M. O. Coastal flooding will disproportionately impact people on river deltas. Nat. Commun. 11, 1–8 (2020).Article 
    CAS 

    Google Scholar 
    Renaud, F. G. et al. Tipping from the Holocene to the Anthropocene: How threatened are major world deltas? Curr. Opin. Environ. Sustain. 5, 644–654 (2013).Article 

    Google Scholar 
    Santos, M. J. & Dekker, S. C. Locked‑in and living delta pathways in the Anthropocene. Sci. Rep. 10, 19598 (2020).Tessler, Z. D. et al. Profiling risk and sustainability in coastal deltas of the world. Science 349, 638–643 (2015).CAS 
    Article 

    Google Scholar 
    Kennedy, C. M., Oakleaf, J. R., Theobald, D. M., Baruch-Mordo, S. & Kiesecker, J. Managing the middle: A shift in conservation priorities based on the global human modification gradient. Glob. Change Biol. 25, 811–826 (2019).Article 

    Google Scholar 
    Seto, K. C. Exploring the dynamics of migration to mega-delta cities in Asia and Africa: Contemporary drivers and future scenarios. Glob. Environ. Change 21, S94–S107 (2011).Article 

    Google Scholar 
    Carpenter, S. R., Stanley, E. H. & Vander Zanden, M. J. State of the World’s Freshwater Ecosystems: Physical, Chemical, and Biological Changes. Annu. Rev. Environ. Resour. 36, 75–99 (2011).Article 

    Google Scholar 
    Dugan, P. J. et al. Fish migration, dams, and loss of ecosystem services in the mekong basin. Ambio 39, 344–348 (2010).Article 

    Google Scholar 
    Notebaert, B., Broothaerts, N. & Verstraeten, G. Evidence of anthropogenic tipping points in fluvial dynamics in Europe. Glob. Planet. Change 164, 27–38 (2018).Article 

    Google Scholar 
    Vörösmarty, C. J. et al. Global threats to human water security and river biodiversity. Nature 467, 555–561 (2010).Article 
    CAS 

    Google Scholar 
    Haberl, H. et al. Quantifying and mapping the human appropriation of net primary production in earth’s terrestrial ecosystems. Proc. Natl. Acad. Sci. 104, 12942–12947 (2007).CAS 
    Article 

    Google Scholar 
    Minderhoud, P. S. J. et al. The relation between land use and subsidence in the Vietnamese Mekong delta. Sci. Total Environ. 634, 715–726 (2018).CAS 
    Article 

    Google Scholar 
    Venter, O. et al. Global terrestrial Human Footprint maps for 1993 and 2009. Sci. Data 3, 160067 (2016).Article 

    Google Scholar 
    FAO. AQUASTAT Database. (2022). Available at: https://www.fao.org/aquastat/statistics/query/index.html. (Accessed: 14th February 2022)Chau, N. D. G., Sebesvari, Z., Amelung, W. & Renaud, F. G. Pesticide pollution of multiple drinking water sources in the Mekong Delta, Vietnam: evidence from two provinces. Environ. Sci. Pollut. Res. 22, 9042–9058 (2015).CAS 
    Article 

    Google Scholar 
    Phien-wej, N., Giao, P. H. & Nutalaya, P. Land subsidence in Bangkok, Thailand. Eng. Geol. 82, 187–201 (2006).Article 

    Google Scholar 
    Käkönen, M. Mekong Delta at the crossroads: more control or adaptation? Ambio 37, 205–212 (2008).Article 

    Google Scholar 
    Smajgl, A. et al. Responding to rising sea levels in the Mekong Delta. Nat. Clim. Change 5, 167–174 (2015).Article 

    Google Scholar 
    Schneider, P. & Asch, F. Rice production and food security in Asian Mega deltas—A review on characteristics, vulnerabilities and agricultural adaptation options to cope with climate change. J. Agron. Crop Sci. 206, 491–503 (2020).Article 

    Google Scholar 
    Gibson, L. et al. Primary forests are irreplaceable for sustaining tropical biodiversity. Nature 478, 378–381 (2011).CAS 
    Article 

    Google Scholar 
    Davis, M., Faurby, S. & Svenning, J. C. Mammal diversity will take millions of years to recover from the current biodiversity crisis. Proc. Natl. Acad. Sci. 115, 11262–11267 (2018).CAS 
    Article 

    Google Scholar 
    Arowolo, A. O., Deng, X., Olatunji, O. A. & Obayelu, A. E. Assessing changes in the value of ecosystem services in response to land-use/land-cover dynamics in Nigeria. Sci. Total Environ. 636, 597–609 (2018).CAS 
    Article 

    Google Scholar 
    Lang, Y. & Song, W. Quantifying and mapping the responses of selected ecosystem services to projected land use changes. Ecol. Indic. 102, 186–198 (2019).Article 

    Google Scholar 
    Tilman, D., Reich, P. B. & Isbell, F. Biodiversity impacts ecosystem productivity as much as resources, disturbance, or herbivory. Proc. Natl. Acad. Sci. 109, 10394–10397 (2012).CAS 
    Article 

    Google Scholar 
    Liang, J. et al. Positive biodiversity-productivity relationship predominant in global forests. Science 354, aaf8957 (2016).Diaz, R. J. & Rosenberg, R. Spreading dead zones and consequences for marine ecosystems. Science 321, 926–929 (2008).CAS 
    Article 

    Google Scholar 
    Dalin, C., Konar, M., Hanasaki, N., Rinaldo, A. & Rodriguez-Iturbe, I. Evolution of the global virtual water trade network. Proc. Natl. Acad. Sci. 109, 5989–5994 (2012).CAS 
    Article 

    Google Scholar 
    Van Asselen, S., Verburg, P. H., Vermaat, J. E. & Janse, J. H. Drivers of wetland conversion: A global meta-analysis. PLoS One 8, e81292 (2013).Davidson, N. C., Fluet-Chouinard, E. & Finlayson, C. M. Global extent and distribution of wetlands: trends and issues. Mar. Freshw. Res. 69, 620–627 (2018).Article 

    Google Scholar 
    Gordon, L. J., Finlayson, C. M. & Falkenmark, M. Managing water in agriculture for food production and other ecosystem services. Agric. Water Manag. 97, 512–519 (2010).Article 

    Google Scholar 
    Syvitski, J. P. M. & Kettner, A. J. Sediment flux and the anthropocene. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 369, 957–975 (2011).Article 

    Google Scholar 
    Nienhuis, J. H. et al. Global-scale human impact on delta morphology has led to net land area gain. Nature 577, 514–518 (2020).CAS 
    Article 

    Google Scholar 
    Cinner, J. E. et al. Bright spots among the world’s coral reefs. Nature 535, 416–419 (2016).CAS 
    Article 

    Google Scholar 
    Stott, I., Soga, M., Inger, R. & Gaston, K. J. Land sparing is crucial for urban ecosystem services. Front. Ecol. Environ. 13, 387–393 (2015).Article 

    Google Scholar 
    Caldwell, R. L. et al. A global delta dataset and the environmental variables that predict delta formation. Earth Surf. Dyn. Discuss. 7, 773–787 (2019).Article 

    Google Scholar 
    Lehner, B., Verdin, K. & Jarvis, A. New global hydrography derived from spaceborne elevation data. Eos (Washington DC) 89, 93–94 (2008).USGS. HYDRO1k Elevation Derivative Database. https://doi.org/10.5066/F77P8WN0 (2000).CIESIN – Center for International Earth Science Information Network Columbia University. Gridded Population of the World, Version 4 (GPWv4): Population Density, Revision 11. Palisades, NY: NASA Socioeconomic Data and Applications Center (SEDAC) https://doi.org/10.7927/H4JW8BX5 (2018).Venter, O. et al. Last of the Wild Project, Version 3 (LWP-3): 2009 Human Footprint, 2018 Release. NASA Socioeconomic Data and Applications Center https://doi.org/10.7927/H46T0JQ4 (2018).Venter, O. et al. Sixteen years of change in the global terrestrial human footprint and implications for biodiversity conservation. Nat. Commun. 7, 1–11 (2016).Article 
    CAS 

    Google Scholar 
    Zeileis, A., Leisch, F., Hornik, K. & Kleiber, C. strucchange: An R package for testing for structural change in linear regression models. J. Stat. Softw. 7, 1–38 (2002).Article 

    Google Scholar 
    Monti, S., Tamayo, P., Mesirov, J. & Golub, T. Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data. Mach. Learn. 52, 91–118 (2003).Article 

    Google Scholar 
    Reader, M. O. et al. Zenodo. https://doi.org/10.5281/zenodo.6346472 (2022).QGIS Development Team. QGIS Geographic Information System. Open Source Geospatial Foundation Project. (2019).R Core Team. R: A language and environment for statistical computing. (2020). More

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    Mycelium chemistry differs markedly between ectomycorrhizal and arbuscular mycorrhizal fungi

    Melillo, J. M. et al. Soil warming and carbon-cycle feedbacks to the climate system. Science 298, 2173–2176 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    Stockmann, U. et al. The knowns, known unknowns and unknowns of sequestration of soil organic carbon. Agric. Ecosyst. Environ. 164, 80–99 (2013).CAS 
    Article 

    Google Scholar 
    Sokol, N. W., Sanderman, J. & Bradford, M. A. Pathways of mineral-associated soil organic matter formation: Integrating the role of plant carbon source, chemistry, and point of entry. Glob. Chang. Biol. 25, 12–24 (2019).PubMed 
    Article 

    Google Scholar 
    Krull, E. S., Baldock, J. A. & Skjemstad, J. O. Importance of mechanisms and processes of the stabilisation of soil organic matter for modelling carbon turnover. Funct. Plant Biol. 30, 207–222 (2003).PubMed 
    Article 

    Google Scholar 
    Langley, J. A. & Hungate, B. A. Mycorrhizal controls on belowground litter quality. Ecology 84, 2302–2312 (2003).Article 

    Google Scholar 
    Strickland, M. S., Osburn, E., Lauber, C., Fierer, N. & Bradford, M. A. Litter quality is in the eye of the beholder: Initial decomposition rates as a function of inoculum characteristics. Funct. Ecol. 23, 627–636 (2009).Article 

    Google Scholar 
    Cou ̂teaux, M. M., Bottner, P. & Berg, B. Litter decomposition, climate and litter quality. Trends Ecol. Evol. 10, 63–66 (1995).Article 

    Google Scholar 
    Prescott, C. E. Litter decomposition: What controls it and how can we alter it to sequester more carbon in forest soils? Biogeochemistry 101, 133–149 (2010).CAS 
    Article 

    Google Scholar 
    Frey, S. D., Lee, J., Melillo, J. M. & Six, J. The temperature response of soil microbial efficiency and its feedback to climate. Nat. Clim. Chang. 3, 395–398 (2013).CAS 
    Article 

    Google Scholar 
    Fernandez, C. W., Heckman, K., Kolka, R. & Kennedy, P. G. Melanin mitigates the accelerated decay of mycorrhizal necromass with peatland warming. Ecol. Lett. 22, 498–505 (2019).PubMed 
    Article 

    Google Scholar 
    Brovkin, V. et al. Plant-driven variation in decomposition rates improves projections of global litter stock distribution. Biogeosciences 9, 565–576 (2012).CAS 
    Article 

    Google Scholar 
    Aponte, C., García, L. V., & Marañón, T. Tree species effect on litter decomposition and nutrient release in mediterranean oak forests changes over time. Ecosystems 15, 1204–1218 (2012).CAS 
    Article 

    Google Scholar 
    Hättenschwiler, S. & Jørgensen, H. B. Carbon quality rather than stoichiometry controls litter decomposition in a tropical rain forest. J. Ecol. 98, 754–763 (2010).Article 
    CAS 

    Google Scholar 
    van der Heijden, M. G., Martin, F. M., Selosse, M.-A. & Sanders, I. R. Mycorrhizal ecology and evolution: the past, the present, and the future. N. Phytol. 205, 1406–1423 (2015).Article 
    CAS 

    Google Scholar 
    Lin, G., McCormack, M. L., Ma, C. & Guo, D. Similar below-ground carbon cycling dynamics but contrasting modes of nitrogen cycling between arbuscular mycorrhizal and ectomycorrhizal forests. N. Phytol. 213, 1440–1451 (2017).CAS 
    Article 

    Google Scholar 
    Högberg, M. N. & Högberg, P. Extramatrical ectomycorrhizal mycelium contributes one‐third of microbial biomass and produces, together with associated roots, half the dissolved organic carbon in a forest soil. N. Phytol. 154, 791–795 (2002).Article 

    Google Scholar 
    Leake, J. et al. Networks of power and influence: the role of mycorrhizal mycelium in controlling plant communities and agroecosystem functioning. Can. J. Bot. 82, 1016–1045 (2004).Article 

    Google Scholar 
    Bååth, E., Nilsson, L. O., Göransson, H. & Wallander, H. Can the extent of degradation of soil fungal mycelium during soil incubation be used to estimate ectomycorrhizal biomass in soil? Soil Biol. Biochem. 36, 2105–2109 (2004).Article 
    CAS 

    Google Scholar 
    Kaiser, C. et al. Exploring the transfer of recent plant photosynthates to soil microbes: Mycorrhizal pathway vs direct root exudation. N. Phytol. 205, 1537–1551 (2015).CAS 
    Article 

    Google Scholar 
    Konvalinková, T., Püschel, D., Řezáčová, V., Gryndlerová, H. & Jansa, J. Carbon flow from plant to arbuscular mycorrhizal fungi is reduced under phosphorus fertilization. Plant Soil 419, 319–333 (2017).Article 
    CAS 

    Google Scholar 
    Ouimette, A. P. et al. Accounting for carbon flux to mycorrhizal fungi may resolve discrepancies in forest carbon budgets. Ecosystems 23, 715–729 (2019).Article 
    CAS 

    Google Scholar 
    Wallander, H., Nilsson, L. O., Hagerberg, D. & Bååth, E. Estimation of the biomass and seasonal growth of external mycelium of ectomycorrhizal fungi in the field. N. Phytol. 151, 753–760 (2001).CAS 
    Article 

    Google Scholar 
    Allen, M. F. & Kitajima, K. Net primary production of ectomycorrhizas in a California forest. Fungal Ecol. 10, 81–90 (2014).Article 

    Google Scholar 
    Godbold, D. L. et al. Mycorrhizal hyphal turnover as a dominant process for carbon input into soil organic matter. Plant Soil 281, 15–24 (2006).CAS 
    Article 

    Google Scholar 
    Frey, S. D. Mycorrhizal fungi as mediators of soil organic matter dynamics. Annu. Rev. Ecol. Evol. Syst. 50, 237–259 (2019).Article 

    Google Scholar 
    Brundrett, M. C. & Tedersoo, L. Evolutionary history of mycorrhizal symbioses and global host plant diversity. N. Phytol. 220, 1108–1115 (2018).Article 

    Google Scholar 
    Soudzilovskaia, N. A. et al. Global mycorrhizal plant distribution linked to terrestrial carbon stocks. Nat. Commun. 10, 5077 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Phillips, R. P., Brzostek, E. & Midgley, M. G. The mycorrhizal‐associated nutrient economy: a new framework for predicting carbon–nutrient couplings in temperate forests. N. Phytol. 199, 41–51 (2013).CAS 
    Article 

    Google Scholar 
    Miyauchi, S. et al. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nat. Commun. 11, 5125 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Harley, J. L. Fungi in ecosystems. J. Ecol. 59, 653 (1971).Article 

    Google Scholar 
    Fernandez, C. W., Langley, J. A., Chapman, S., McCormack, M. L. & Koide, R. T. The decomposition of ectomycorrhizal fungal necromass. Soil Biol. Biochem. 93, 38–49 (2016).CAS 
    Article 

    Google Scholar 
    Fernandez, C. W. & Koide, R. T. Initial melanin and nitrogen concentrations control the decomposition of ectomycorrhizal fungal litter. Soil Biol. Biochem. 77, 150–157 (2014).CAS 
    Article 

    Google Scholar 
    Trofymow, J. A. The Canadian Institute Decomposition Experiment (CIDET): project and site establishment report / J.A. Trofymow and the CIDET Working Group. (1998).Gholz, H. L., Wedin, D. A., Smitherman, S. M., Harmon, M. E. & Parton, W. J. Long-term dynamics of pine and hardwood litter in contrasting environments: Toward a global model of decomposition. Glob. Chang. Biol. 6, 751–765 (2000).Article 

    Google Scholar 
    Kögel-Knabner, I. The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biol. Biochem 34, 139–162 (2002).Article 

    Google Scholar 
    Zeglin, L. H. & Myrold, D. D. Fate of decomposed fungal cell wall material in organic horizons of old-growth douglas-fir forest soils. Soil Sci. Soc. Am. J. 77, 489–500 (2013).CAS 
    Article 

    Google Scholar 
    Kleber, M. et al. Mineral-organic associations: formation, properties, and relevance in soil environments. in. Adv. Agron. 130, 1–140 (2015).Article 

    Google Scholar 
    Fortin, J. A. et al. Arbuscular mycorrhiza on root-organ cultures. Can. J. Bot. 80, 1–20 (2002).CAS 
    Article 

    Google Scholar 
    Declerck, S., Séguin, S. & Dalpé, Y. The monoxenic culture of Arbuscular Mycorrhizal fungi as a tool for germplasm collections. in In Vitro Culture of Mycorrhizas 17–30 (Springer-Verlag, 2005).Lalaymia, I. & Declerck, S. The Mycorrhizal Donor Plant (MDP) in vitro culture system for the efficient colonization of whole plants. 2146, (Springer US, 2020).Crous, P. W., Verkley, G. J. M., Groenewald, J. Z. & Houbraken, J. Westerdijk Laboratory Manual Series 1: Fungal Biodiversity. (2019).Tuomi, M. et al. Leaf litter decomposition-Estimates of global variability based on Yasso07 model. Ecol. Modell. 220, 3362–3371 (2009).CAS 
    Article 

    Google Scholar 
    Clemmensen, K. E. et al. Carbon sequestration is related to mycorrhizal fungal community shifts during long‐term succession in boreal forests. N. Phytol. 205, 1525–1536 (2015).CAS 
    Article 

    Google Scholar 
    Averill, C., Turner, B. L. & Finzi, A. C. Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage. Nature 505, 543–545 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Staddon, P. L., Ramsey, C. B., Ostle, N., Ineson, P. & Fitter, A. H. Rapid turnover of hyphae of mycorrhizal fungi determined by AMS microanalysis of 14C. Science 300, 1138–1140 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Adamczyk, B., Sietiö, O., Biasi, C. & Heinonsalo, J. Interaction between tannins and fungal necromass stabilizes fungal residues in boreal forest soils. N. Phytol. 223, 16–21 (2019).Article 

    Google Scholar 
    Davison, J. et al. Plant functional groups associate with distinct arbuscular mycorrhizal fungal communities. N. Phytol. 226, 1117–1128 (2020).Article 

    Google Scholar 
    Liski, J., Palosuo, T., Peltoniemi, M. & Sievänen, R. Carbon and decomposition model Yasso for forest soils. Ecol. Modell. 189, 168–182 (2005).CAS 
    Article 

    Google Scholar 
    Guendehou, G. H. S. et al. Decomposition and changes in chemical composition of leaf litter of five dominant tree species in a West African tropical forest. Trop. Ecol. 55, 207–220 (2014).
    Google Scholar 
    Paterson, E. et al. Labile and recalcitrant plant fractions are utilised by distinct microbial communities in soil: Independent of the presence of roots and mycorrhizal fungi. Soil Biol. Biochem. 40, 1103–1113 (2008).CAS 
    Article 

    Google Scholar 
    Cotrufo, M. F., Wallenstein, M. D., Boot, C. M., Denef, K. & Paul, E. The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant inputs form stable soil organic matter? Glob. Chang. Biol. 19, 988–995 (2013).PubMed 
    Article 

    Google Scholar 
    Xia, J. et al. Global patterns in Net Primary Production allocation regulated by environmental conditions and forest stand age: a model‐data comparison. J. Geophys. Res. Biogeosciences 124, 2039–2059 (2019).Article 

    Google Scholar 
    Malhi, Y., Doughty, C. & Galbraith, D. The allocation of ecosystem net primary productivity in tropical forests. Philos. Trans. R. Soc. B Biol. Sci. 366, 3225–3245 (2011).CAS 
    Article 

    Google Scholar 
    Tedersoo, L., May, T. W. & Smith, M. E. Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza 20, 217–263 (2010).PubMed 
    Article 

    Google Scholar 
    Rinaldi, A. C., Comandini, O. & Kuyper, T. W. Ectomycorrhizal fungal diversity: separating the wheat from the chaff. Fungal Divers 33, 1–45 (2008).
    Google Scholar 
    Krüger, M., Krüger, C., Walker, C., Stockinger, H. & Schüßler, A. Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level. N. Phytol. 193, 970–984 (2012).Article 

    Google Scholar 
    Lee, E.-H., Eo, J.-K., Ka, K.-H. & Eom, A.-H. Diversity of arbuscular mycorrhizal fungi and their roles in ecosystems. Mycobiology 41, 121–125 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schüβler, A., Schwarzott, D. & Walker, C. A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol. Res. 105, 1413–1421 (2001).Article 

    Google Scholar 
    Declerck, S., Strullu, D. G. & Plenchette, C. Monoxenic culture of the intraradical forms of Glomus sp. isolated from a tropical ecosystem: a proposed methodology for germplasm collection. Mycologia 90, 579 (1998).Article 

    Google Scholar 
    Voets, L. et al. Extraradical mycelium network of arbuscular mycorrhizal fungi allows fast colonization of seedlings under in vitro conditions. Mycorrhiza 19, 347–356 (2009).PubMed 
    Article 

    Google Scholar 
    von Lützow, M. et al. SOM fractionation methods: Relevance to functional pools and to stabilization mechanisms. Soil Biol. Biochem. 39, 2183–2207 (2007).Article 
    CAS 

    Google Scholar 
    Davidson, E. A., Galloway, L. F. & Strand, M. K. Assessing available carbon: Comparison of techniques across selected forest soils. Commun. Soil Sci. Plant Anal. 18, 45–64 (1987).CAS 
    Article 

    Google Scholar 
    Trumbore, S. E., Vogel, J. S. & Southon, J. R. AMS 14C measurements of fractionated soil organic matter: an approach to deciphering the soil carbon cycle. Radiocarbon 31, 644–654 (1989).Article 

    Google Scholar 
    Henriksen, T. & Breland, T. Evaluation of criteria for describing crop residue degradability in a model of carbon and nitrogen turnover in soil. Soil Biol. Biochem 31, 1135–1149 (1999).CAS 
    Article 

    Google Scholar 
    Schnitzer, M. & Schuppli, P. Method for the sequential extraction of organic matter from soils and soil fractions. Soil Sci. Soc. Am. J. 53, 1418–1424 (1989).CAS 
    Article 

    Google Scholar 
    Ryan, M. G., Melillo, J. M. & Ricca, A. A comparison of methods for determining proximate carbon fractions of forest litter. Can. J . Res. 20, 166–171 (1990).Article 

    Google Scholar 
    Wieder, R. K. & Starr, S. T. Quantitative determination of organic fractions in highly organic, Sphagnum peat soils. Commun. Soil Sci. Plant Anal. 29, 847–857 (1998).CAS 
    Article 

    Google Scholar 
    Xu, G. et al. Differential responses of soil hydrolytic and oxidative enzyme activities to the natural forest conversion. Sci. Total Environ. 716, 136414 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Viskari, T. et al. Improving Yasso15 soil carbon model estimates with ensemble adjustment Kalman filter state data assimilation. Geosci. Model Dev. 13, 5959–5971 (2020). https://doi.org/10.5194/gmd-13-5959-2020.CAS 
    Article 

    Google Scholar 
    Anderson, M. J. Permutational multivariate analysis of variance (PERMANOVA). Wiley StatsRef: Statistics Reference Online, https://doi.org/10.1002/9781118445112.stat07841 (2014).Anderson, M. J., Ellingsen, K. E. & McArdle, B. H. Multivariate dispersion as a measure of beta diversity. Ecol. Lett. 9, 683–693 (2006).PubMed 
    Article 

    Google Scholar 
    Tomczak, M. & Tomczak, E. The need to report effect size estimates revisited. An overview of some recommended measures of effect size. Trends Sport Sci. 1, 19–25 (2014).
    Google Scholar 
    Kattge, J. et al. TRY – a global database of plant traits. Glob. Chang. Biol. 17, 2905–2935 (2011).PubMed Central 
    Article 

    Google Scholar 
    Engemann, K. et al. A plant growth form dataset for the New World. Ecology 97, 3243 (2016).CAS 
    PubMed 
    Article 

    Google Scholar  More

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    Large size in aquatic tetrapods compensates for high drag caused by extreme body proportions

    Drag coefficients of plesiosaurs, ichthyosaurs and modern cetaceansAt equal Reynolds numbers (same body length and same flow velocity), the total drag coefficients of plesiosaurs (Cd) are higher than the estimated values for ichthyosaurs and modern cetaceans (Fig. 1a). The limbless bodies, however, display similar Cd in all three groups and are even lower-than-average in the long-necked plesiosaurs, indicating that the limbs are responsible for the observed high Cd. The limbs of plesiosaurs contribute to more than 20% of their total drag coefficient: up to 32.2% in the basal Meyerasaurus and averaging 25% in derived plesiosaurs, with no major differences between plesiosaur morphotypes. In parvipelvian ichthyosaurs the contribution of the limbs to Cd is 11.2–15.6%, compared to 8.7–14.3% in modern cetaceans. Some of the living taxa we include provide a functional reference for this analysis. Our computed drag coefficient for the bottlenose dolphin model (Cd = 0.00413 at Re = 107) for example, is consistent with the estimates from a gliding living dolphin33 (Cd = 0.0034 at Re = 9.1 × 106) and other static CFD simulations34 (Cd = 0.00413 at Re = 107). It is worth noting that these values are, as expected, lower than estimates obtained from kinematic models, as motion is not accounted for35. In a former study, drag coefficients for a plesiosaur (Cryptoclidus), two ichthyosaurs and various cetaceans were obtained from rigid models in water tanks36. However, the pressure drag component (Cp) was likely overestimated due to the proximity of the models to the air–water interface, and thus are not directly comparable to ours.Fig. 1: Comparison of the drag coefficient of derived plesiosaurs, ichthyosaurs and cetaceans.a Total drag coefficient computed for the full models including the limbs (‘body + limbs’, circles) and the limbless models (‘body’, squares). Average (point) and range (bar) shown for calculations at Re = 5 × 106–107. The derived short-necked plesiosaurs are highlighted in orange; the parvipelvian ichthyosaurs in blue and the extant cetaceans in red. A basal plesiosaur included as a reference is highlighted in purple. b Representative two-dimensional plots of the flow velocity magnitude at Re = 5 × 106 (inlet velocity of 5 ms−1) in lateral view. For dorsal view see Supplementary Fig. 1. Images of Tursiops and the three ichthyosaurs modified from Gutarra et al.29.Full size imageIn all models across the various clades, velocity plots display a stagnation point at the anterior tip of the model, a thin velocity gradient along the body corresponding to the boundary layer, an area of higher velocity around the greatest diameter and a low velocity wake behind the body, characteristic features of a fully developed external flow (Fig. 1b, Supplementary Fig. 1). The acceleration of flow results in areas of low pressure (Supplementary Fig. 2), while high pressure areas are observed where stagnation occurs. Our CFD methodology has been previously validated against experimental data from slender torpedo-like shapes26 and has been shown to provide a reliable distribution of internal drag components29 essential when dealing with streamlined bodies35. In all our simulations, the proportion of frictional and pressure drag was consistent with the expected values for slender geometries31: most of the drag originated from skin friction with a minor pressure drag component (Supplementary Fig. 2). The relatively larger limbs of plesiosaurs (Supplementary Table 1) produce a small increase in skin friction (Supplementary Fig. 2a), but a large increase in the pressure drag coefficient (Supplementary Fig. 2b), indicating that the latter largely explains differences in total drag coefficient between the groups. These effects might be explained by the low local Reynolds number of the flippers (resulting from a small chord length) producing high local Cd relative to the rest of the body31, alongside interference drag (i.e. drag caused by the interaction of flow fields where limbs and body meet), which might be higher for larger flippers.Effect of body shape and body size on drag-related costs of steady swimmingWhen comparing morphologies at the same volume (proxy for body mass) and the same velocity, to focus on the effect of shape alone, derived plesiosaurs produce on average 30% more drag than parvipelvian ichthyosaurs and modern cetaceans (Fig. 2a, Supplementary Table 3; two-sample t-tests p  0.05). In these conditions, the drag-related costs of steady swimming of plesiosaurs fall within the range observed in both modern cetaceans and ichthyosaurs. Normalised against a 2.85 m-long Tursiops, the COTdrag for derived plesiosaurs ranges from 0.42, estimated for the large elasmosaur Thalassomedon, to 1.41 in the medium-sized Dolichorhynchops. In the parvipelvians, COTdrag spans from 0.33 estimated for the large Temnodontosaurus, to 1.76 in a 2.5 m-long Stenopterygius. Cetaceans show a smaller lower limit, because they include the largest animal in our sample, a 16 m-long humpback whale, with a COTdrag of 0.13 compared to Tursiops. The estimated cetacean upper COTdrag limit is 1.54 for a 1.9 m Tursiops. On the other hand, comparisons of the total drag power (Pdrag, i.e., the non-mass normalised version of COTdrag) for the same speed of 1 ms−1 (Fig. 3), show a different trend. Pdrag is highest for Megaptera, higher than in any fossil taxa included in this study, and is lowest in Tursiops. Thalassomedon is comparable both in total drag power and COTdrag to the killer whale. Similarly, the thalassophonean pliosaurid Liopleurodon matches the elasmosaurian Hydrotherosaurus in having a similarly low mass-normalised COTdrag but requiring about 4× more total drag power than Tursiops. Smaller forms like the polycotylid Dolichorhynchops and the thunnosaurian Ophthalmosaurus resemble the extant bottlenose dolphin in having a relatively high COTdrag and low total power.Fig. 3: Comparative plot of mass-normalised drag power and total drag power.Values of mass-normalised drag power (i.e., drag per unit of volume or COTdrag calculated as in Fig. 2b) in grey, and non-mass-normalised total drag power, in black, for an array of derived plesiosaurs, parvipelvian ichthyosaurs and modern cetaceans compared at the same inlet velocity of 1 ms−1. Error bars represent minimum and maximum values accounting for taxon body size variation (see Supplementary Data). Values are normalised to the results for Tursiops.Full size imageThus, in contrast to the volume-normalised simulations, differences between animals at their life-size scale are mainly influenced by size. For example, medium-sized plesiosaurs and ichthyosaurs, such as Dolichorhynchops and Ophthalmosaurus, have values of COTdrag close to that of a dolphin, while large plesiosaurs like Thalassomedon are more like the parvipelvian ichthyosaur Temnodontosaurus and a modern Orcinus. It is worth noting that the inflow velocity of 1 ms−1, is a reference velocity used for comparative purposes, and is not equivalent to the optimal cruising speed (i.e. speed at which COT is minimum16). This parameter is known to vary little in nature, with most vertebrates displaying values of preferred speed between 1–2 ms−1 regardless of body size40,41,42, which means it is reasonable to assume all tested taxa, regardless of their size, were able to swim at this velocity. Using a different reference velocity (2 ms−1) has no effect on the relative values of drag per unit of volume and the mass-normalised drag power (Supplementary Fig. 3; Supplementary Data). A reduction of mass-normalised drag-related costs of cruising as body size increases is selectively advantageous, as energy savings can be used to extend foraging and mating range, increase swimming speed and fuel other activities42,43.Our analysis shows that for highly aquatic tetrapods, size dominates over shape in affecting the drag-related costs of steady locomotion. This is because COTdrag (i.e., the balance of drag to volume) is highly sensitive to surface/volume proportion (Fig. 2f), and so is much influenced by isometry in streamlined animals.Interplay between neck anatomy and body size in plesiosaur dragSimulations at constant Reynolds number (i.e., comparing models at same total length and same flow velocity), show that necks up to 5× the length of the trunk do not increase substantially the total drag coefficient. Longer neck ratios up to 7× were found to impact the drag coefficient by as little as 3% (Fig. 4a). We estimated a 4–10% increase in skin friction drag coefficient for neck ratios of 3–7×, but also a comparable reduction in pressure drag resulting in almost no change in the total drag coefficient. A previous CFD-based study also found no differences in drag coefficient between plesiosaur models with variable neck proportions20, but further comparison is not possible because of great differences in the order of magnitude of Cd, the use of a different scaling reference area and the lack of information on skin and pressure drag20. Here, we have shown that long necks produce only a small increase in skin friction, although not as great as previously speculated25,30, and this is nullified by reduced pressure drag.Fig. 4: Influence of neck length and its interaction with body size on the drag-related costs of swimming in plesiosaurs.a Total drag coefficient and skin friction drag coefficient for an array of hypothetical plesiosaurs with varying neck ratios computed at Re = 5 × 106 (same total length and inflow velocity). b Drag per unit of trunk volume computed for the same array of models scaled at the same trunk length and tested at the same speed of 1 ms−1. The hypothetical models were created by modifying the length in the model of the basal plesiosaur Meyerasaurus victor which has a neck ratio of 0.87×. The limits of the trunk (which extends along the torso and includes the edges of the pectoral and pelvic girdles) are shown in red in the rendered models. c Three-dimensional models of a wide array of plesiosaurs, in dorsal view, at their life-size dimensions, showing the differences in body proportions and sizes. The limits of the trunk in the models (defined as in b) are coloured by group. Basal plesiosaurs are highlighted in purple. Among the derived groups, thalassophonean plesiosaurs (derived pliosaurid plesiosaurs) are highlighted in light orange, polycotylid plesiosaurs in dark orange and elasmosaurid plesiosaurs in green. d Scatterplot of trunk length (cm) and neck ratio showing the relative drag per unit of trunk volume as a gradient of colour for each taxon analysed and for the plot area in between (contour lines represent the interpolated values of drag per unit of volume). e Plot of the relative drag per unit of trunk volume versus the trunk length showing results highlighted by group. Line plots at the right-hand side show the range for each group. The D/Vtr and the trunk length show a significant negative correlation (Pearson’s correlation coefficient calculated with log-transformed variables, p = 2.28 × 10−7, R2 = −0.92). A small version of the fitted power curve (regression equation (y=69.76{x}^{-0.94})) is shown on the right upper corner. The grey area around the curve represents a confidence interval of 95%. All values in b, d and e are normalized to the results for the Meyerasaurus model.Full size imageNext, we explored the impact of neck proportions on drag-related costs of swimming in simulations where the size factor is removed. We found that if trunk dimensions are kept constant while the neck is enlarged, the drag per unit of trunk volume does not change appreciably for neck ratios up to 2×. However, longer neck proportions did impact resistive forces. This was moderate for a 3× ratio, with 12% more drag per unit of trunk volume, but became more substantial for longer necks, with 22%, 35% and 59% excess drag for necks of 4×, 5× and 7× respectively (Fig. 4b). This means that elasmosaurine elasmosaurs, with necks commonly 3–4× the length of the trunk23 might have experienced higher drag than other plesiosaurs of similar trunk dimensions.To test if the ‘long neck effect’ remains when body size is accounted for, we compared the relative amount of drag-per-unit-trunk-volume (D/Vtr) in a wide sample of plesiosaurs (Fig. 4c) at life-size scale for a constant velocity of 1 ms−1, including three species with neck ratios above 2×: Styxosaurus (2.76×), Hydrotherosaurus (3.18×) and Albertonectes (3.72×), the last being the elasmosaur with the longest reported neck44. Our results show great variability in D/Vtr. Small-bodied plesiosaurs such as Plesiosaurus, Meyerasaurus and Dolichorhynchops generated up to six times more D/Vtr than the largest plesiosaurs, Kronosaurus and Aristonectes (Fig. 4d, e). Comparisons per group show that both basal plesiosaurs and derived polycotylids, the groups with the smallest specimens, produced generally higher D/Vtr. Moreover, we did not find substantial differences between elasmosaurs and thalassophonean pliosauroids (Fig. 4e, Supplementary Table 4; all two-sample t-tests p  > 0.05). Both groups had similarly low ranges of D/Vtr regardless of neck length, lower on average than in polycotylids. These results stand even if we exclude Aristonectes, which belongs to the aristonectines, an elasmosaur subfamily with reduced neck length23,45. Further comparisons by morphotype show no significant differences between short-necked pliosauromorphs (here arbitrarily including plesiosaurs with neck ratios below 2×) and long-necked plesiosauromorphs (Supplementary Table 4, all two-sample t-tests p  > 0.05). The highest values of D/Vtr occur in animals with trunk lengths of 100 cm or less, followed by a steep decrease between 100–150 cm and a steadier decrease in longer trunks. This indicates a strong negative correlation between trunk dimensions and D/Vtr (Pearson’s product-moment correlation between the log-transformed variables, adjusted r2 = −0.92, p = 2.28 × 10−7). The curve that best describes this relationship is the power equation, D/Vtr = 69.76 × Trunk length−0.944 (Fig. 4e), an almost inversely proportional relationship, consistent with the streamlined nature of these animals for which skin friction drag is dominant.Polycotylids and thalassophonean pliosaurs, both derived pliosauromorph plesiosaurs9,21, share the same general body proportions9,21,46, but the latter had larger bodies and therefore needed less power in relation to their muscles to move at the same speed. Elasmosaurs on the other hand, despite their disparate morphologies, were no different from thalassophonean pliosaurs in their drag-related costs of forward swimming (Fig. 4c–e) and therefore they were likely to have been equally efficient cruisers.Earlier research suggested that, even if long necks did not add extra drag during forward swimming, speed in elasmosaurs would have been limited to avoid added drag when their necks bent20. However, when the neck is bent in living forms, the course of swimming changes, as does the flow direction, but the body remains streamlined in the direction of incoming flow. For example, sea lions perform non-powered turns initiated by the head in which the body glides smoothly in a curved position, limiting deceleration47. Further biomechanical research is needed to understand the role of plesiosaur necks in manoeuvrability and other aspects of swimming performance, as well as how these were influenced by shape and flexibility. The well-established idea that long-necked plesiosaurs were sluggish, slow swimmers7,30 is thus not supported here, not because long necks did not increase drag20, but because body size overrode this drag excess.Long necks evolved in large-bodied plesiosaurs: implications for dragWe analysed trends of body size and neck proportion in a wider sample of sauropterygians, including plesiosaurian and non-plesiosaurian Triassic sauropterygians. Long necks (neck ratio > 3×) occur in taxa with trunk lengths > 150 cm, whereas most sauropterygians had neck ratios of ≤ 2× (Fig. 5a). The great plasticity of body proportions of sauropterygians before and after their transition to a pelagic lifestyle after the Triassic has been well documented21,23,46, but this is the first time that neck and body size have been explored in the context of swimming performance for such a wide sample. We show that overall, sauropterygians and particularly plesiosaurs, mainly explored neck morphologies with little or no effect on drag costs and did not enter morphospaces that were suboptimal for aquatic locomotion (i.e., corresponding to small trunks with long necks; Fig. 5a). In fact, ancestral state reconstruction for trunk length shows that the ancestor of elasmosaurs was likely around 180 cm long and had a relatively short neck with a ratio smaller than 2× (Fig. 5b, c). This indicates that large trunks preceded neck elongation in elasmosaurs and suggests that extreme proportions might have been favoured by a release of hydrodynamic constraints.Fig. 5: Evolutionary trends of neck proportions and body size in Sauropterygia and their implications for the drag-related costs of swimming.a Bivariate plot of the length of trunk and the neck ratio of 79 sauropterygian taxa. Polygons in different colours show area occupied by the main sauropterygian groups. The functional trends describing the effect of each axis are based on results from flow simulations. On the top of this graph, a univariate plot shows the distribution and mean values of trunk length for each group. b, c Phenograms showing the disparity of trunk length (b) and neck ratio (c) in sauropterygians through time. The branches corresponding to basal Plesiosauria (including Rhomaleosauridae and Plesiosauridae), thalassophonean pliosaurs, polycotylids and elasmosaurs are highlighted (colour coding as in a). d, e Sauropterygian trees showing the evolutionary rates for trunk length (d) and neck ratio (e) represented by colour gradient (see Supplementary Fig. 5 for an alternative analysis to 5d using the log10-transformed trunk length). Consensus trees show average results from analyses of 20 cal3-dated trees (see Supplementary Figs. 4 and 6 for analysis on Hedman-dated trees). Rates are based on the mean scalar evolutionary rate parameter.Full size imageWe next explored evolutionary rates of relative neck length and trunk length in sauropterygians. The pattern of trunk length evolution is consistent with a heterogeneous rates model, not a homogeneous Brownian motion model (log Bayes Factor48 (BF)  > 5 in 100% of the sampled trees and > 10 in 92.5%, Supplementary Table 5). Analysis of non-transformed trunk data shows that through the evolution of Sauropterygia, there was a general increase in trunk length with some higher rates, in Triassic nothosauroids, Jurassic rhomaleosaurids and Cretaceous aristonectine elasmosaurs (Fig. 5d; Supplementary Fig. 4a). Additionally, analysis of the log10-transformed trunk data highlights variation in the small-to-medium size ranges and reveals high rates in Triassic eosauropterygians (Supplementary Figs. 5 and 6). The largest trunks evolved independently in two groups, thalassophonean pliosaurids and elasmosaurid plesiosauroids, with no evidence of high rates in the former. In the plesiosauroids, rates are not particularly high in the basal branches, but they are very high in derived aristonectines, and rates for the whole clade were significantly higher than the background rate in 40% of randomisation tests (Supplementary Fig. 7 and Table 6). A progressive increase in body mass over evolutionary time has been described for various clades of aquatic mammals49 and seems to be a common hallmark of the aquatic adaptation to marine pelagic lifestyles in secondarily aquatic tetrapods44. Whether body size reaches a plateau as is the case in cetaceans49 and what constraints influence the evolutionary patterns of size in plesiosaurs remains unexplored. Against this general trend, some derived plesiosaurs, such as polycotylids, saw a reduction in body size, which might have been related to pressures on niche selection, such as adaptation to specific prey, the need for higher manoeuvrability or other ecological factors. As shown earlier, small sizes require lower amounts of total power for a given speed, and therefore would be favoured if for example food resources were limited. This suggests that, in spite of the energy advantages of large size in terms of reduced mass-specific drag29 and metabolic rates49,50, which make it a common adaptation to the pelagic mode of life, other constraints limiting very large sizes were also at work50,51.A heterogeneous evolutionary rates model for neck proportion is also strongly supported (log BF  > 5 in 100% of the sampled trees and > 10 in 45%, Supplementary Table 5). Fast rates are consistently seen at the base of Pistosauroidea (including some Triassic forms and plesiosaurs) and, interestingly, also within elasmosaurs (Fig. 5e; Supplementary Fig. 4b). The neck proportions of elasmosaurs were found to evolve at a faster pace than the background rate in 90% of analyses (randomisation test p-value < 0.001 in 80% and < 0.01 in 10% of the sampled trees; Supplementary Fig. 7 and Table 6). Very fast rates in elasmosaurs are concentrated in the most derived branches (i.e., Euelasmosauridia from the late Upper Cretaceous52) and represent both rapid neck elongation in elasmosaurines and rapid neck shortening in weddellonectians (i.e., aristonectines and closely related taxa52). Additionally, various other independent instances of relative shortening of the neck occurred during the evolution of Sauropterygia, most notably in placodonts, pliosaurs and polycotylids, but these are not associated with high rates.Our findings contrast with a previous study23 which did not identify any significant evolutionary rate shifts in the neck ratio across Sauropterygia. Here we use a larger number of taxa and a different model fitting approach, which might account for these discrepancies. The association between very long necks and large trunks, along with our flow simulations results and the evidence of high rates in the elongation of necks in elasmosaurines (Fig. 5e), suggests that neck elongation was facilitated by large body sizes. The question remains why neck ratios did not evolve longer than 4×. According to our data, hydrodynamic constraints might have operated against the selection of such long necks. However, it is possible that the primary function for which they were selected, which is still debated30,53, did not require necks with those characteristics. Neck anatomy is likely to be the result of a compromise between different functions/constraints, one of them being hydrodynamic, as shown by the results presented herein. More

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    A perspective of scale differences for studying the green total factor productivity of Chinese laying hens

    Minimum distance to weak efficient frontierBriec and Charnes et al. first proposed the Minimum distance to weak efficient frontier (MinDW) model39,40, which can be expressed as (m + n) linear programming ((m) is the number of input indicators and (n) is the number of output indicators), assuming that the input variable is (x) and the output variable is (y). The specific formula is shown in Eq. (1):$$ begin{aligned} & max beta_{z} ,z = 1,2, ldots ,m + n \ & s.t.left{ begin{gathered} sumnolimits_{j = 1}^{q} {alpha_{j} x_{rj} + beta_{z} e_{r} le x_{rk} ,r = 1,2, ldots ,m} hfill \ sumnolimits_{j = 1}^{q} {alpha_{j} x_{ij} + beta_{z} e_{i} ge y_{ik} ,i = 1,2, ldots ,n} hfill \ alpha_{j} ge 0 hfill \ end{gathered} right. \ end{aligned} $$
    (1)
    (e_{r}) and (e_{i}) are constants. In the programming formula, only one (e) is equal to 1, and the others are 0, that is shown in Eq. (2):$$ begin{aligned} & e_{r} = 1;{text{ if}}; , r = z; , e_{r} = 0 , ;{text{if}}; , r ne z \ & e_{i} = 1 , ;{text{if}}; , i = z – m; , e_{r} = 0 , ;{text{if}}; , i ne z – m \ end{aligned} $$
    (2)
    The efficiency value of model is expressed as Eq. (3):$$ theta_{z}^{*} = frac{{1 – frac{1}{m}sumnolimits_{r = 1}^{m} {frac{{beta_{z}^{*} e_{r} }}{{x_{rk} }}} }}{{1 + frac{1}{n}sumnolimits_{i = 1}^{n} {frac{{beta_{z}^{*} e_{i} }}{{y_{ik} }}} }} $$
    (3)
    The efficiency value of MinDW model is expressed as (theta_{max }^{*} = max (theta_{z}^{*} ,z = 1,2, cdots ,m + n)), and the maximum efficiency value corresponds to the minimum (beta^{*}), that is the nearest distance to the frontier.This paper uses the MinDW model with negative output to conduct empirical analysis. The method can be expressed as (m + n + d) linear programming ((m) is the number of inputs, (n) is the number of desirable output, (d) is the number of unexpected output), assuming that the input variable is (x), the desirable output variable is (y), and the undesirable output variable is (f). The specific formula is shown in Eq. (4):$$ begin{aligned} & max beta_{z} ,z = 1,2, ldots ,m + n + d \ & s.t.left{ begin{gathered} sumnolimits_{j = 1}^{q} {alpha_{j} x_{rj} + beta_{z} e_{r} le x_{rk} ,r = 1,2, ldots ,m} hfill \ sumnolimits_{j = 1}^{q} {alpha_{j} x_{ij} – beta_{z} e_{i} ge y_{ik} ,i = 1,2, ldots ,n} hfill \ sumnolimits_{j = 1}^{q} {alpha_{j} x_{lj} + beta_{z} e_{l} le f_{lk} ,l = 1,2, ldots ,d} hfill \ alpha_{j} ge 0 hfill \ end{gathered} right. \ end{aligned} $$
    (4)
    (e_{r}), (e_{i}) and (e_{l}) are constants. In the programming formula, only one (e) is equal to 1, and the others are 0, that is shown in Eq. (5):$$ begin{aligned} & e_{r} = 1;{text{ if}}; , r = z; , e_{r} = 0 , ;{text{if}}; , r ne z \ & e_{i} = 1 , ;{text{if }};i = z – m; , e_{r} = 0 , ;{text{if}}; , i ne z – m \ & e_{l} = 1 , ;{text{if}}; , l = z – m – n; , e_{l} = 0 , ;{text{if}}; , l ne z – m – n \ end{aligned} $$
    (5)
    The efficiency value of model is expressed as Eq. (6):$$ theta_{z}^{*} = frac{{1 – frac{1}{m}sumnolimits_{r = 1}^{m} {frac{{beta_{z}^{*} e_{r} }}{{x_{rk} }}} }}{{1 + frac{1}{n + d}left( {sumnolimits_{i = 1}^{n} {frac{{beta_{z}^{*} e_{i} }}{{y_{ik} }}} + sumnolimits_{l = 1}^{d} {frac{{beta_{z}^{*} e_{l} }}{{f_{lk} }}} } right)}} $$
    (6)
    The efficiency value of MinDW model is expressed as (theta_{max }^{*} = max (theta_{z}^{*} ,z = 1,2, cdots ,m + n + d)), and the maximum efficiency value corresponds to the minimum (beta^{*}), which means the nearest distance to the frontier.The efficiency value of MinDW model will not be less than the efficiency value of directional distance function model with any direction vector or other distance types (such as radial model and SBM model). In other words, the efficiency value of MinDW model is the largest. Combined with the above process, we can define the common boundary ((beta^{meta*})) and the model is as Eq. (7):$$ begin{aligned} & beta^{meta*} = max frac{{1 – frac{1}{m}sumnolimits_{r = 1}^{m} {frac{{beta_{z} e_{r} }}{{x_{rk} }}} }}{{1 + frac{1}{n + d}left( {sumnolimits_{i = 1}^{n} {frac{{beta_{z} e_{i} }}{{y_{ik} }}} + sumnolimits_{l = 1}^{d} {frac{{beta_{z} e_{l} }}{{f_{lk} }}} } right)}} \ & s.t.left{ begin{gathered} sumnolimits_{j = 1}^{{q_{m} }} {alpha_{j} x_{rj} + beta_{z} e_{r} le x_{rk} ,r = 1,2, cdots ,m} hfill \ sumnolimits_{j = 1}^{{q_{m} }} {alpha_{j} x_{ij} – beta_{z} e_{i} ge y_{ik} ,i = 1,2, cdots ,n} hfill \ sumnolimits_{j = 1}^{{q_{m} }} {alpha_{j} x_{lj} + beta_{z} e_{l} le f_{lk} ,l = 1,2, cdots ,d} hfill \ alpha_{j} ge 0 hfill \ end{gathered} right. \ end{aligned} $$
    (7)
    Similarly, the efficiency value of DMU relative to the scale frontier ((beta^{scale*})) can be obtained by the Eq. (8):$$ begin{aligned} & beta^{scale*} = max frac{{1 – frac{1}{m}sumnolimits_{r = 1}^{m} {frac{{beta_{z} e_{r} }}{{x_{rk} }}} }}{{1 + frac{1}{n + d}left( {sumnolimits_{i = 1}^{n} {frac{{beta_{z} e_{i} }}{{y_{ik} }}} + sumnolimits_{l = 1}^{d} {frac{{beta_{z} e_{l} }}{{f_{lk} }}} } right)}} \ & s.t.left{ begin{gathered} sumnolimits_{j = 1}^{{q_{s} }} {alpha_{j} x_{rj} + beta_{z} e_{r} le x_{rk} ,r = 1,2, ldots ,m} hfill \ sumnolimits_{j = 1}^{{q_{s} }} {alpha_{j} x_{ij} – beta_{z} e_{i} ge y_{ik} ,i = 1,2, ldots ,n} hfill \ sumnolimits_{j = 1}^{{q_{s} }} {alpha_{j} x_{lj} + beta_{z} e_{l} le f_{lk} ,l = 1,2, ldots ,d} hfill \ alpha_{j} ge 0 hfill \ end{gathered} right. \ end{aligned} $$
    (8)
    Finally, in the common frontier model, the technology gap ratio (TGR) is equal to the ratio of the efficiency value of the common frontier to the scale frontier41. The formula is as Eq. (9):$$ TGR^{MinDW} = frac{{beta^{meta*} }}{{beta^{scale*} }} $$
    (9)
    (beta^{meta*}) and (beta^{scale*}) represent the optimal solution of formula (7) and formula (8), respectively. Obviously, (0 le TGR le 1). TGR is used to measure the distance between the optimal production technology and the potential optimal technology of a group, and identify whether there are any differences in LHG under different groups. The closer the TGR is to 1, the closer the technology level is to the optimal potential technology level. Conversely, it shows the larger gap between the technology level and the potential optimal technology level.Metafrontier-Malmquist–Luenberger indexMalmquist productivity index is widely used in the study of dynamic efficiency change trend, and has good adaptability to multiple input–output data and panel data analysis. The actual production process often contains unexpected output. After Chung et al. proposed Malmquist–Luenberger (ML) index, any Malmquist index with undesired output can be called ML index42. Oh constructed the Global-Malmquist–Luenberger index43. All the evaluated DMUs are included in the global reference set, which avoids the phenomenon of infeasible solution in VRS. The global reference set constructed in this paper is as Eqs. (10)–(11):$$ Q^{G} left( x right) = Q^{1} left( {x^{1} } right) cup Q^{2} left( {x^{2} } right) cup cdots cup Q^{T} left( {x^{T} } right) $$
    (10)
    $$ Q^{t} left( {x^{t} } right) = left{ {left( {y^{t} ,f^{t} } right)left| {x^{t} ;can;produce} right.;left( {y^{t} ,f^{t} } right)} right} $$
    (11)
    This paper takes MML index as the LHG.$$ begin{aligned} MML_{t – 1}^{t} & = sqrt {frac{{1 – D_{t – 1} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{t – 1} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}} times frac{{1 – D_{t} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{t} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}}} \ & = sqrt {frac{{1 – D_{t – 1} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}}{{1 – D_{t} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}} times frac{{1 – D_{t – 1} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{t} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}} \ & ;;;;; times frac{{1 – D_{t} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{t – 1} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}} \ end{aligned} $$
    (12)
    Next, it further decompose the MML index into efficiency change (EC) and technology change (TC). The specific formula is shown in Eqs. (13)–(14):$$ TC_{t – 1}^{t} = sqrt {frac{{1 – D_{t – 1} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}}{{1 – D_{t} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}} times frac{{1 – D_{t – 1} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{t} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}} $$
    (13)
    $$ EC_{t – 1}^{t} = frac{{1 – D_{t} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{t – 1} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}} $$
    (14)
    where (left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} } right)) and (left( {x^{t} ,y^{t} ,f^{t} } right)) represent the input, expected output and unexpected output of t-1 and t, respectively. (TC_{t – 1}^{t}) is the devotion to LHG raise of DMU’s technical progress from (t – 1) to (t). And (EC_{t – 1}^{t}) represents the devotion to LHG raise of DMU’s efficiency improvement from (t – 1) to (t). The higher the value is, the larger the devotion is. The (MML) index is recorded as (MI). The value of (MI) is the LHG. The green total factor productivity index of laying hens breeding under the common frontier and scale frontier are as Eqs. (15)–(16):$$ metaMI_{t – 1}^{t} = sqrt {frac{{1 – D_{{_{t – 1} }}^{m} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{{_{t – 1} }}^{m} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}} times frac{{1 – D_{{_{t} }}^{m} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{{_{t} }}^{m} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}}} $$
    (15)
    $$ groupMI_{t – 1}^{t} = sqrt {frac{{1 – D_{{_{t – 1} }}^{g} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{{_{t – 1} }}^{g} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}} times frac{{1 – D_{{_{t} }}^{g} left( {x^{t} ,y^{t} ,f^{t} ;y^{t} , – f^{t} } right)}}{{1 – D_{{_{t} }}^{g} left( {x^{t – 1} ,y^{t – 1} ,f^{t – 1} ;y^{t – 1} , – f^{t – 1} } right)}}} $$
    (16)
    For the DMUs with scale heterogeneity, we can measure the technology gap between the group frontier and the common frontier, which is caused by the specific group structure.Data and variablesBased on the research of the existing literature36, this paper selects five indexes to build the input–output indicator system. Details are as below:

    1.

    Input variables:

    (1)

    Quantity of concentrated forage. Mainly includes seeds of crops and their by-products.

    (2)

    Quantity of grain consumption. Quantity of grain consumed is the quantity of grain consumed by laying hens when they are raised. For example: corn, sorghum, broken rice, wheat, barley, wheat bran, etc.

    (3)

    Material expenses. The sum of water and fuel power costs, labor costs, and medical epidemic prevention fees. Water and fuel power costs include water, electricity, coal and other fuel power costs; labor costs mean the human management cost of each laying hen from the brood stage to the laying stage; medical and epidemic prevention costs include the cost of disease prevention and control.

    2.

    Positive output Main product production, which is the egg production per layer.

    3.

    Negative output Total discharge. According to the calculation method of The Manual of Pollutant Discharge Coefficient, Eq. (17) is used to calculate the COD, TN, and the TP of each layer. Then, according to the calculation method of class GB3838-2002 water quality standard in V, Eq. (18) is used to calculate the total discharge.

    $$ POLLUTANTS = FP(FD) times Days $$
    (17)
    $$ TOTAL , POLLUTANTS = frac{COD}{{40}} + frac{TN}{2} + frac{TP}{{0.4}} $$
    (18)
    where, (FP(FD)) is the pollution discharge coefficient and the (Days) is the average raising days. Descriptive statistics of input and output indicators are shown in Table 1.Table 1 Descriptive statistics of input and output indicators.Full size tableThe quantity of concentrate, the quantity of food consumed, the cost of labor, the cost of medical treatment all come from “National Agricultural Product Cost and Benefit Data Compilation”. The pollutant discharge coefficient of laying hens is derived from “The Manual of Pollutant Discharge Coefficient”. According to the definition of scale in above two materials, a small scale 300–1000 laying hens, a medium scale 1000–10,000 laying hens, and a large scale greater than 10,000 laying hens are grouped to calculate cost efficiency.From 2004 to 2018, this paper selects 24 major egg-producing provinces (municipalities) in China as samples, after eliminating singular data in the three scales and averaging the missing data, the final small-scale group is left with 7 provinces including Liaoning, Shandong, Henan, Heilongjiang, Jilin, Shanxi, and Shaanxi; the medium-scale group is the remaining 21 provinces of Beijing, Hebei, Jiangsu, Liaoning, Shandong, Tianjin, Zhejiang, Anhui, Henan, Heilongjiang, Jilin, Hubei, Inner Mongolia, Shanxi, Yunnan, Gansu, Ningxia, Shaanxi, Sichuan, Xinjiang, Chongqing; the large-scale group has 18 provinces, including Beijing, Fujian, Guangdong, Henan, Jiangsu, Liaoning, Shandong, Tianjin, Anhui, Henan, Heilongjiang, Hubei, Jilin, Shanxi, Yunnan, Gansu, Sichuan and Chongqing.As is shown in Table 2, after dividing the provinces by region, the eastern region has 10 provinces (municipalities): Liaoning, Shandong, Beijing, Hebei, Jiangsu, Tianjin, Zhejiang, Fujian, Guangdong, Henan. The central region has 7 provinces (autonomous region): Henan, Heilongjiang, Jilin, Shanxi, Anhui, Hubei, Inner Mongolia. The western region has 7 provinces (municipalities): Shaanxi, Gansu, Ningxia, Sichuan, Xinjiang, Chongqing, Yunnan.Table 2 Samples selected from 2004–2018.Full size table More

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    Collegiality pays and biodiversity struggles

    Animals such as this orangutan in Indonesia are endangered because of illegal deforestation.Credit: Jami Tarris/Future Publishing via Getty

    Funding battles stymie plan to protect global biodiversityScientists are frustrated with slow progress towards a new deal to protect the natural world. Government officials from around the globe met in Geneva, Switzerland, on 14–29 March to find common ground on a draft of the deal, known as the post-2020 global biodiversity framework, but discussions stalled.The framework so far sets out 4 broad goals, including slowing species extinction, and 21 mostly quantitative targets, such as protecting at least 30% of the world’s land and seas. It is part of an international treaty known as the United Nations Convention on Biological Diversity, and aims to address the global biodiversity crisis, which could see one million plant and animal species go extinct in the next few decades.Many who were at the meeting say that disagreements over funding for biodiversity conservation were the main hold-up in negotiations. For example, the draft deal proposed that US$10 billion of funding per year should flow from developed nations to low- and middle-income countries to help them to implement the biodiversity framework. But many think this is not enough.Negotiators say they will now have to meet again before a highly anticipated UN biodiversity summit later this year, where the deal was to be signed.‘Collegiality’ influences researchers’ promotion prospectsUniversities in North America often consider how well researchers interact with each other when making decisions about who gets promoted, a study has found, even though these factors are not formally acknowledged in review guidelines.A researcher’s performance is usually assessed according to three pillars: research, teaching and service. But in recent years, there has been a push from some academics to add another pillar: collegiality. Many say that the concepts of cooperation, collaboration and respect, which broadly fall under the definition of collegiality, are important to the functioning of laboratories and research teams.DeDe Dawson, an academic librarian at the University of Saskatchewan in Saskatoon, Canada, and colleagues analysed more than 860 review, promotion and tenure documents from different departments at 129 universities in the United States and Canada to get a sense of how often collegiality is taken into account.The study, published on 6 April (D. Dawson et al. PLoS ONE 17, e0265506; 2022), found that the concept of collegiality was widespread: the word ‘collegiality’ and related terms, such as ‘citizenship’ or ‘professionalism’, appeared 507 times in 213 of the documents, suggesting that it was often taken into account in evaluations. But just 85 documents included a definition of the term, and fewer still explained how it was measured or used in assessments.

    Source: D. Dawson et al. PLoS ONE 17, e0265506 (2022)

    Collegiality was mentioned most often in research-intensive institutions (see ‘Academia’s fourth pillar’). The authors say that this could be because the behaviour involved is valued in research groups.Dawson and her colleagues warn that relying on collegiality in performance reviews without adequate guidance could introduce bias, as those in charge fill in the blanks with their own definitions.“We need to make sure that we don’t use collegiality to exclude others that may communicate or interact differently,” says Sujay Kaushal, a geologist at the University of Maryland in College Park, who has previously studied collegiality. More

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    Expanding ocean food production under climate change

    United Nations. World Population Prospects: The 2017 Revision, Key Findings and Advance Tables. Working Paper No. ESA/P/WP/248 (UN-DESA, 2017).Costello, C. et al. The future of food from the sea. Nature 588, 95–100 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    IPCC. IPCC Special Report on the Ocean and Cryosphere in a Changing Climate (2019).FAO. Mapping Supply and Demand for Animal-Source Foods to 2030 (2011).Foley, J. A. et al. Global consequences of land use. Science 309, 570–574 (2005).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    DeFries, R. S., Rudel, T., Uriarte, M. & Hansen, M. Deforestation driven by urban population growth and agricultural trade in the twenty-first century. Nat. Geosci. 3, 178–181 (2010).ADS 
    CAS 
    Article 

    Google Scholar 
    Rockström, J. et al. Future water availability for global food production: the potential of green water for increasing resilience to global change. Water Resour. Res. 45, W00A12 (2009).Article 

    Google Scholar 
    IPCC. IPCC Special Report on Climate Change and Land (2019).Poore, J. & Nemecek, T. Reducing food’s environmental impacts through producers and consumers. Science 360, 987–992 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    FAO. The State of World Fisheries and Aquaculture 2020: Sustainability in Action (2020).Bryndum‐Buchholz, A. et al. Twenty-first-century climate change impacts on marine animal biomass and ecosystem structure across ocean basins. Glob. Change Biol. 25, 459–472 (2019).ADS 
    Article 

    Google Scholar 
    Cheung, W. W. L., Dunne, J., Sarmiento, J. L. & Pauly, D. Integrating ecophysiology and plankton dynamics into projected maximum fisheries catch potential under climate change in the Northeast Atlantic. ICES J. Mar. Sci. 68, 1008–1018 (2011).Article 

    Google Scholar 
    Froehlich, H. E., Gentry, R. R. & Halpern, B. S. Global change in marine aquaculture production potential under climate change. Nat. Ecol. Evol. 2, 1745–1750 (2018).PubMed 
    Article 

    Google Scholar 
    Handisyde, N., Telfer, T. C. & Ross, L. G. Vulnerability of aquaculture-related livelihoods to changing climate at the global scale. Fish Fish. 18, 466–488 (2017).Article 

    Google Scholar 
    Szuwalski, C. S. & Hollowed, A. B. Climate change and non-stationary population processes in fisheries management. ICES J. Mar. Sci. 73, 1297–1305 (2016).Article 

    Google Scholar 
    Pinsky, M. L. et al. Preparing ocean governance for species on the move. Science 360, 1189–1191 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Gaines, S. D. et al. Improved fisheries management could offset many negative effects of climate change. Sci. Adv. 4, eaao1378 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Free, C. M. et al. Realistic fisheries management reforms could mitigate the impacts of climate change in most countries. PLoS ONE 15, e0224347 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Clapp, J. Food self-sufficiency: making sense of it, and when it makes sense. Food Policy 66, 88–96 (2017).Article 

    Google Scholar 
    Barange, M., Bahri, T., Beveridge, M. & Cochrane, K. L. Impacts of Climate Change on Fisheries and Aquaculture: Synthesis of Current Knowledge, Adaptation and Mitigation Options. Fisheries and Aquaculture Technical Paper No. 627 (FAO, 2018).Lester, S. E. et al. Marine spatial planning makes room for offshore aquaculture in crowded coastal waters. Nat. Commun. 9, 945 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cottrell, R. S., Blanchard, J. L., Halpern, B. S., Metian, M. & Froehlich, H. E. Global adoption of novel aquaculture feeds could substantially reduce forage fish demand by 2030. Nat. Food 1, 301–308 (2020).Article 

    Google Scholar 
    Hua, K. et al. The future of aquatic protein: implications for protein sources in aquaculture diets. One Earth 1, 316–329 (2019).ADS 
    Article 

    Google Scholar 
    Chavanne, H. et al. A comprehensive survey on selective breeding programs and seed market in the European aquaculture fish industry. Aquacult. Int. 24, 1287–1307 (2016).Article 

    Google Scholar 
    Troell, M., Jonell, M. & Henriksson, P. J. G. Ocean space for seafood. Nat. Ecol. Evol. 1, 1224–1225 (2017).PubMed 
    Article 

    Google Scholar 
    European Union. Commission Regulation (EC) No 710/2009 of 5 August 2009 Amending Regulation (EC) No 889/2008 laying down detailed rules for the implementation of Council Regulation (EC) No 834/2007, as regards laying down detailed rules on organic aquaculture animal and seaweed production. http://data.europa.eu/eli/reg/2009/710/oj (2009).Golden, C. D. et al. Aquatic foods to nourish nations. Nature 598, 315–320 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Davies, I. P. et al. Governance of marine aquaculture: pitfalls, potential, and pathways forward. Mar. Policy 104, 29–36 (2019).Article 

    Google Scholar 
    Gentry, R. R. et al. Exploring the potential for marine aquaculture to contribute to ecosystem services. Rev. Aquacult. 12, 499–512 (2020).Article 

    Google Scholar 
    Troell, M. et al. Ecological engineering in aquaculture — potential for integrated multi-trophic aquaculture (IMTA) in marine offshore systems. Aquaculture 297, 1–9 (2009).Article 

    Google Scholar 
    Froehlich, H. E., Jacobsen, N. S., Essington, T. E., Clavelle, T. & Halpern, B. S. Avoiding the ecological limits of forage fish for fed aquaculture. Nat. Sustain. 1, 298–303 (2018).Article 

    Google Scholar 
    Øverland, M., Mydland, L. T. & Skrede, A. Marine macroalgae as sources of protein and bioactive compounds in feed for monogastric animals. J. Sci. Food Agric. 99, 13–24 (2019).PubMed 
    Article 
    CAS 

    Google Scholar 
    Besson, M. et al. Environmental impacts of genetic improvement of growth rate and feed conversion ratio in fish farming under rearing density and nitrogen output limitations. J. Clean. Prod. 116, 100–109 (2016).Article 

    Google Scholar 
    Froehlich, H. E., Runge, C. A., Gentry, R. R., Gaines, S. D. & Halpern, B. S. Comparative terrestrial feed and land use of an aquaculture-dominant world. Proc. Natl Acad. Sci. USA 115, 5295–5300 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aguilar-Manjarrez, J., Soto, D., Brummett, R. E. Aquaculture Zoning, Site Selection and Area Management under the Ecosystem Approach to Aquaculture (FAO, 2017).Soto, D. et al. In Impacts Of Climate Change on Fisheries and Aquaculture: Synthesis of Current Knowledge, Adaptation and Mitigation Options Ch. 26 (FAO, 2018).Darwin, C. The Variation of Animals and Plants Under Domestication (John Murray, 1868).Gjedrem, T., Robinson, N. & Rye, M. The importance of selective breeding in aquaculture to meet future demands for animal protein: a review. Aquaculture 350–353, 117–129 (2012).Article 

    Google Scholar 
    Antonello, J. et al. Estimates of heritability and genetic correlation for body length and resistance to fish pasteurellosis in the gilthead sea bream (Sparus aurata L.). Aquaculture 298, 29–35 (2009).Article 

    Google Scholar 
    Saillant, E., Dupont-Nivet, M., Haffray, P. & Chatain, B. Estimates of heritability and genotype–environment interactions for body weight in sea bass (Dicentrarchus labrax L.) raised under communal rearing conditions. Aquaculture 254, 139–147 (2006).Article 

    Google Scholar 
    Klinger, D. H., Levin, S. A. & Watson, J. R. The growth of finfish in global open-ocean aquaculture under climate change. Proc. R. Soc. B 284, 20170834 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Salayo, N. D., Perez, M. L., Garces, L. R. & Pido, M. D. Mariculture development and livelihood diversification in the Philippines. Mar. Policy 36, 867–881 (2012).Article 

    Google Scholar 
    Boyce, D. G., Lotze, H. K., Tittensor, D. P., Carozza, D. A. & Worm, B. Future ocean biomass losses may widen socioeconomic equity gaps. Nat. Commun. 11, 2235 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Sumaila, U. R. et al. Benefits of the Paris Agreement to ocean life, economies, and people. Sci. Adv. 5, eaau3855 (2019).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    United Nations. Transforming Our World: The 2030 Agenda for Sustainable Development (United Nations, 2017).Hilborn, R. et al. Effective fisheries management instrumental in improving fish stock status. Proc. Natl Acad. Sci. USA 117, 2218–2224 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Free, C. M. et al. Impacts of historical warming on marine fisheries production. Science 363, 979–983 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Costello, C. et al. Global fishery prospects under contrasting management regimes. Proc. Natl Acad. Sci. USA 113, 5125–5129 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ye, Y. & Gutierrez, N. L. Ending fishery overexploitation by expanding from local successes to globalized solutions. Nat. Ecol. Evol. 1, 0179 (2017).Article 

    Google Scholar 
    Leape, J. et al. Technology, Data and New Models for Sustainably Managing Ocean Resources (World Resources Institute, 2020).Anderson, C. R. et al. Scaling up from regional case studies to a global harmful algal bloom observing system. Front. Mar. Sci. 6, 250 (2019).Article 

    Google Scholar 
    Dunn, D. C., Maxwell, S. M., Boustany, A. M. & Halpin, P. N. Dynamic ocean management increases the efficiency and efficacy of fisheries management. Proc. Natl Acad. Sci. USA 113, 668–673 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    FAO. Aquaculture Development: 7. Aquaculture Governance and Sector Development (2017).Oyinlola, M. A., Reygondeau, G., Wabnitz, C. C. C., Troell, M. & Cheung, W. W. L. Global estimation of areas with suitable environmental conditions for mariculture species. PLoS ONE 13, e0191086 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Jackson, A. Fish in-fish out ratio explained. Aquacult. Eur. 34, 5–10 (2009).
    Google Scholar 
    Tacon, A. G. J. & Metian, M. Feed matters: satisfying the feed demand of aquaculture. Rev. Fish. Sci. Aquacult. 23, 1–10 (2015).Article 

    Google Scholar 
    Tacon, A. G. J. & Metian, M. Global overview on the use of fish meal and fish oil in industrially compounded aquafeeds: trends and future prospects. Aquaculture 285, 146–158 (2008).CAS 
    Article 

    Google Scholar 
    World Bank. Population, Total (2020); https://data.worldbank.org/indicator/SP.POP.TOTLEdwards, P., Zhang, W., Belton, B. & Little, D. C. Misunderstandings, myths and mantras in aquaculture: its contribution to world food supplies has been systematically over reported. Mar. Policy 106, 103547 (2019).Article 

    Google Scholar 
    Roberts, P. Conversion Factors for Estimating the Equivalent Live Weight of Fisheries Products (The Food and Agriculture Organization of the United Nations, 1998).R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021).Kaschner, K. et al. AquaMaps: Predicted Range Maps for Aquatic Species https://www.aquamaps.org/ (2019).García Molinos, J. et al. Climate velocity and the future global redistribution of marine biodiversity. Nat. Clim. Change 6, 83–88 (2016).ADS 
    Article 

    Google Scholar 
    Cashion, T., Le Manach, F., Zeller, D. & Pauly, D. Most fish destined for fishmeal production are food-grade fish. Fish Fish. 18, 837–844 (2017).Article 

    Google Scholar 
    Froehlich, H. E., Gentry, R. R. & Halpern, B. S. Synthesis and comparative analysis of physiological tolerance and life-history growth traits of marine aquaculture species. Aquaculture 460, 75–82 (2016).Article 

    Google Scholar 
    Thorson, J. T., Munch, S. B., Cope, J. M. & Gao, J. Predicting life history parameters for all fishes worldwide. Ecol. Appl. 27, 2262–2276 (2017).PubMed 
    Article 

    Google Scholar 
    Froese, R. & Pauly, D. FishBase http://www.fishbase.org (2021).Palomares, M. & Pauly, D. SeaLifeBase http://www.sealifebase.org (2019).FAO. Cultured Aquatic Species (2019).Dunne, J. P. et al. GFDL’s ESM2 global coupled climate–carbon Earth system models. Part I: physical formulation and baseline simulation characteristics. J. Clim. 25, 6646–6665 (2012).ADS 
    Article 

    Google Scholar 
    Dunne, J. P. et al. GFDL’s ESM2 global coupled climate–carbon Earth system models. Part II: carbon system formulation and baseline simulation characteristics. J. Clim. 26, 2247–2267 (2013).ADS 
    Article 

    Google Scholar 
    Song, Z. et al. Centuries of monthly and 3-hourly global ocean wave data for past, present, and future climate research. Sci. Data 7, 226 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gentry, R. R. et al. Mapping the global potential for marine aquaculture. Nat. Ecol. Evol. 1, 1317–1324 (2017).PubMed 
    Article 

    Google Scholar 
    Barton, A. et al. Impacts of coastal acidification on the Pacific Northwest shellfish industry and adaptation strategies implemented in response. Oceanography 25, 146–159 (2015).Article 

    Google Scholar 
    Froehlich, H. E., Smith, A., Gentry, R. R. & Halpern, B. S. Offshore aquaculture: I know it when I see it. Front. Mar. Sci. 4, 154 (2017).Article 

    Google Scholar 
    World Bank. Adjusted Net National Income per Capita (Current US$) (2019); https://data.worldbank.org/indicator/NY.ADJ.NNTY.PC.CDWorld Bank. Pump Price for Diesel Fuel (US$ per liter) (2019); https://data.worldbank.org/indicator/EP.PMP.DESL.CDPiburn, J. wbstats: programmatic access to the World Bank API. R package v.1.0.4 https://cran.r-project.org/web/packages/wbstats/index.html (2018).Rubino, M. (ed.) Offshore Aquaculture in the United States: Economic Considerations, Implications & Opportunities NOAA Technical Memorandum NMFS F/SPO-103 (US Department of Commerce, 2008).Jackson, A. & Newton, R. Project to Model the Use of Fisheries By-products in the Production of Marine Ingredients, with Special Reference to the Omega 3 Fatty Acids EPA and DHA (Institute Of Aquaculture, University Of Stirling And IFFO, 2016). More

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    Changes to the gut microbiota of a wild juvenile passerine in a multidimensional urban mosaic

    Szulkin, M. et al. How to quantify urbanization when testing for urban evolution?. Urban Evol. Biol. https://doi.org/10.1093/oso/9780198836841.003.0002 (2020).Article 

    Google Scholar 
    Slabbekoorn, H. Songs of the city: Noise-dependent spectral plasticity in the acoustic phenotype of urban birds. Anim. Behav. https://doi.org/10.1016/j.anbehav.2013.01.021 (2013).Article 

    Google Scholar 
    Christiansen, N. A., Fryirs, K. A., Green, T. J. & Hose, G. C. The impact of urbanisation on community structure, gene abundance and transcription rates of microbes in upland swamps of Eastern Australia. PLoS ONE https://doi.org/10.1371/journal.pone.0213275 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Alberti, M. et al. Global urban signatures of phenotypic change in animal and plant populations. Proc. Natl. Acad. Sci. USA https://doi.org/10.1073/pnas.1606034114 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    McFall-Ngai, M. M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. https://doi.org/10.1073/pnas.1218525110 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zilber-Rosenberg, I. & Rosenberg, E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. https://doi.org/10.1111/j.1574-6976.2008.00123.x (2008).Article 
    PubMed 

    Google Scholar 
    Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices. Proc. R. Soc. B Biol. Sci. https://doi.org/10.1098/rspb.2018.2448 (2019).Article 

    Google Scholar 
    Jarrett, C., Powell, L. L., McDevitt, H., Helm, B. & Welch, A. J. Bitter fruits of hard labour: diet metabarcoding and telemetry reveal that urban songbirds travel further for lower-quality food. Oecologia https://doi.org/10.1007/s00442-020-04678-w (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zollinger, S. A. et al. Traffic noise exposure depresses plasma corticosterone and delays offspring growth in breeding zebra finches. Conserv. Physiol. https://doi.org/10.1093/conphys/coz056 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sprau, P., Mouchet, A. & Dingemanse, N. J. Multidimensional environmental predictors of variation in avian forest and city life histories. Behav. Ecol. https://doi.org/10.1093/beheco/arw130 (2017).Article 

    Google Scholar 
    Teyssier, A. et al. Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2017.09.035 (2018).Article 
    PubMed 

    Google Scholar 
    Murray, M. H. et al. Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird. PLoS ONE https://doi.org/10.1371/journal.pone.0220926 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fuirst, M., Veit, R. R., Hahn, M., Dheilly, N. & Thorne, L. H. Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus. PLoS ONE https://doi.org/10.1371/journal.pone.0209200 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Phillips, J. N., Berlow, M. & Derryberry, E. P. The effects of landscape urbanization on the gut microbiome: An exploration into the gut of urban and rural white-crowned sparrows. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2018.00148 (2018).Article 

    Google Scholar 
    Berlow, M., Phillips, J. N. & Derryberry, E. P. Effects of urbanization and landscape on gut microbiomes in white-crowned sparrows. Microb. Ecol. https://doi.org/10.1007/s00248-020-01569-8 (2020).Article 
    PubMed 

    Google Scholar 
    Cox, L. M. et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell https://doi.org/10.1016/j.cell.2014.05.052 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Knutie, S. A., Wilkinson, C. L., Kohl, K. D. & Rohr, J. R. Early-life disruption of amphibian microbiota decreases later-life resistance to parasites. Nat. Commun. 8, 1–8 (2017).CAS 
    Article 

    Google Scholar 
    Sudyka, J., Di Lecce, I., Wojas, L., Rowiński, P. & Szulkin, M. Nest-boxes alter the reproductive ecology of urban cavity-nesters in a species-dependent way. https://doi.org/10.32942/OSF.IO/WP9MN.
    Maziarz, M., Broughton, R. K. & Wesołowski, T. Microclimate in tree cavities and nest-boxes: Implications for hole-nesting birds. For. Ecol. Manag. https://doi.org/10.1016/j.foreco.2017.01.001 (2017).Article 

    Google Scholar 
    Thompson, M. J., Capilla-Lasheras, P., Dominoni, D. M., Réale, D. & Charmantier, A. Phenotypic variation in urban environments: mechanisms and implications. Trends Ecol. Evol. 37, 171–182 (2022).CAS 
    Article 

    Google Scholar 
    Salmón, P. et al. Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe. Nat. Commun. 12, 1–14 (2021).ADS 
    Article 

    Google Scholar 
    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. https://doi.org/10.1186/s13059-014-0550-8 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sackey, B. A., Mensah, P., Collison, E. & Sakyi-Dawson, E. Campylobacter, Salmonella, Shigella and Escherichia coli in live and dressed poultry from metropolitan Accra. Int. J. Food Microbiol. https://doi.org/10.1016/S0168-1605(01)00595-5 (2001).Article 
    PubMed 

    Google Scholar 
    Benskin, C. M. W. H., Wilson, K., Jones, K. & Hartley, I. R. Bacterial pathogens in wild birds: A review of the frequency and effects of infection. Biol. Rev. https://doi.org/10.1111/j.1469-185X.2008.00076.x (2009).Article 
    PubMed 

    Google Scholar 
    Hansell, M. & Overhill, R. Bird nests and construction behaviour. Bird Nests Constr. Behav. https://doi.org/10.1017/cbo9781139106788 (2000).Article 

    Google Scholar 
    Siddiqui, S. H., Khan, M., Kang, D., Choi, H. W. & Shim, K. Meta-analysis and systematic review of the thermal stress response: Gallus gallus domesticus show low immune responses during heat stress. Front. Physiol. 13, 31 (2022).Article 

    Google Scholar 
    Sepulveda, J. & Moeller, A. H. The effects of temperature on animal gut microbiomes. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.00384 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kohl, K. D. & Yahn, J. Effects of environmental temperature on the gut microbial communities of tadpoles. Environ. Microbiol. https://doi.org/10.1111/1462-2920.13255 (2016).Article 
    PubMed 

    Google Scholar 
    Teyssier, A. et al. Diet contributes to urban-induced alterations in gut microbiota: Experimental evidence from a wild passerine. Proc. R. Soc. B Biol. Sci. https://doi.org/10.1098/rspb.2019.2182 (2020).Article 

    Google Scholar 
    Benskin, C. M. W. H., Rhodes, G., Pickup, R. W., Wilson, K. & Hartley, I. R. Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch. Mol. Ecol. https://doi.org/10.1111/j.1365-294X.2010.04892.x (2010).Article 
    PubMed 

    Google Scholar 
    Garrett, W. S. et al. Enterobacteriaceae Act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe https://doi.org/10.1016/j.chom.2010.08.004 (2010).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Videvall, E. et al. Early-life gut dysbiosis linked to juvenile mortality in ostriches. BMC Microbiome 8, 1–13 (2020).Article 

    Google Scholar 
    Hooper, L. V. & MacPherson, A. J. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat. Rev. Immunol. https://doi.org/10.1038/nri2710 (2010).Article 
    PubMed 

    Google Scholar 
    Borre, Y. E. et al. Microbiota and neurodevelopmental windows: Implications for brain disorders. Trends Mol. Med. https://doi.org/10.1016/j.molmed.2014.05.002 (2014).Article 
    PubMed 

    Google Scholar 
    Jones, E. L. & Leather, S. R. Invertebrates in urban areas: A review. Eur. J. Entomol. https://doi.org/10.14411/eje.2012.060 (2012).Article 

    Google Scholar 
    Wilkin, T. A., King, L. E. & Sheldon, B. C. Habitat quality, nestling diet, and provisioning behaviour in great tits Parus major. J. Avian Biol. https://doi.org/10.1111/j.1600-048X.2009.04362.x (2009).Article 

    Google Scholar 
    Pollock, C. J., Capilla-Lasheras, P., McGill, R. A. R., Helm, B. & Dominoni, D. M. Integrated behavioural and stable isotope data reveal altered diet linked to low breeding success in urban-dwelling blue tits (Cyanistes caeruleus). Sci. Rep. https://doi.org/10.1038/s41598-017-04575-y (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Davidson, G. L. et al. Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird. Sci. Rep. https://doi.org/10.1038/s41598-020-77256-y (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bodawatta, K. H. et al. Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets. Anim. Microbiome 2021(3), 1–14 (2021).
    Google Scholar 
    Baniel, A. et al. Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas. Microbiome 9, 1–20 (2021).Article 

    Google Scholar 
    Sullam, K. E. et al. Environmental and ecological factors that shape the gut bacterial communities of fish: A meta-analysis. Mol. Ecol. https://doi.org/10.1111/j.1365-294X.2012.05552.x (2012).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martiny, J. B. H. et al. Microbial biogeography: Putting microorganisms on the map. Nat. Rev. Microbiol. https://doi.org/10.1038/nrmicro1341 (2006).Article 
    PubMed 

    Google Scholar 
    Lucass, C., Eens, M. & Müller, W. When ambient noise impairs parent-offspring communication. Environ. Pollut. https://doi.org/10.1016/j.envpol.2016.03.015 (2016).Article 
    PubMed 

    Google Scholar 
    Kight, C. R. & Swaddle, J. P. How and why environmental noise impacts animals: An integrative, mechanistic review. Ecol. Lett. https://doi.org/10.1111/j.1461-0248.2011.01664.x (2011).Article 
    PubMed 

    Google Scholar 
    Cui, B., Gai, Z., She, X., Wang, R. & Xi, Z. Effects of chronic noise on glucose metabolism and gut microbiota-host inflammatory homeostasis in rats. Sci. Rep. https://doi.org/10.1038/srep36693 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Campo, J. L., Gil, M. G. & Dávila, S. G. Effects of specific noise and music stimuli on stress and fear levels of laying hens of several breeds. Appl. Anim. Behav. Sci. https://doi.org/10.1016/j.applanim.2004.08.028 (2005).Article 

    Google Scholar 
    Injaian, A. S., Taff, C. C. & Patricelli, G. L. Experimental anthropogenic noise impacts avian parental behaviour, nestling growth and nestling oxidative stress. Anim. Behav. https://doi.org/10.1016/j.anbehav.2017.12.003 (2018).Article 

    Google Scholar 
    Cui, B. et al. Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: Implications for Alzheimer’s disease. J. Neuroinflammation https://doi.org/10.1186/s12974-018-1223-4 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wei, L. et al. Constant light exposure alters gut microbiota and promotes the progression of steatohepatitis in high fat diet rats. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.01975 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chatelain, M. et al. Replicated, urban-driven exposure to metallic trace elements in two passerines. Sci. Rep. 11, 1–10 (2021).Article 

    Google Scholar 
    Chatelain, M. et al. Urban metal pollution explains variation in reproductive outputs in great tits and blue tits. Sci. Total Environ. 776, 145966 (2021).ADS 
    CAS 
    Article 

    Google Scholar 
    Rosenfeld, C. S. Gut dysbiosis in animals due to environmental chemical exposures. Front. Cell. Infect. Microbiol. 7, 396 (2017).Article 

    Google Scholar 
    Sommer, F. & Bäckhed, F. The gut microbiota-masters of host development and physiology. Nat. Rev. Microbiol. https://doi.org/10.1038/nrmicro2974 (2013).Article 
    PubMed 

    Google Scholar 
    Tomiałojć, L. & Wesołowski, T. Diversity of the Białowieza forest avifauna in space and time. J. Ornithol. https://doi.org/10.1007/s10336-003-0017-2 (2004).Article 

    Google Scholar 
    Corsini, M. et al. Growing in the city: Urban evolutionary ecology of avian growth rates. Evol. Appl. https://doi.org/10.1111/eva.13081 (2021).Article 
    PubMed 

    Google Scholar 
    Teyssier, A., Lens, L., Matthysen, E. & White, J. Dynamics of gut microbiota diversity during the early development of an avian host: Evidence from a cross-foster experiment. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.01524 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tremblay, I., Thomas, D., Blondel, J., Perret, P. & Lambrechts, M. M. The effect of habitat quality on foraging patterns, provisioning rate and nestling growth in Corsican Blue Tits Parus caeruleus. Ibis (Lond 1859). 147, 17–24 (2005).Article 

    Google Scholar 
    Corsini, M., Marrot, P. & Szulkin, M. Quantifying human presence in a heterogeneous urban landscape. Behav. Ecol. https://doi.org/10.1093/beheco/arz128 (2019).Article 

    Google Scholar 
    Corsini, M., Dubiec, A., Marrot, P. & Szulkin, M. Humans and tits in the city: Quantifying the effects of human presence on great tit and blue tit reproductive trait variation. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2017.00082 (2017).Article 

    Google Scholar 
    Kyba, C. C. M. et al. High-resolution imagery of earth at night: New sources, opportunities and challenges. Remote Sens. https://doi.org/10.3390/rs70100001 (2015).Article 

    Google Scholar 
    Maraci, Ö. et al. The gut microbial composition is species-specific and individual-specific in two species of estrildid finches, the Bengalese finch and the zebra finch. Front. Microbiol. https://doi.org/10.3389/fmicb.2021.619141 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Engel, K. et al. Individual- and species-specific skin microbiomes in three different estrildid finch species revealed by 16S amplicon sequencing. Microb. Ecol. https://doi.org/10.1007/s00248-017-1130-8 (2017).Article 
    PubMed 

    Google Scholar 
    Magoč, T. & Salzberg, S. L. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics https://doi.org/10.1093/bioinformatics/btr507 (2011).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal https://doi.org/10.14806/ej.17.1.200 (2011).Article 

    Google Scholar 
    Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.01541-09 (2009).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics https://doi.org/10.1093/bioinformatics/btq461 (2010).Article 
    PubMed 

    Google Scholar 
    Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. https://doi.org/10.1093/nar/gks1219 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    R Core Team. R: A language and environment for statistical computing (R Foundation for Statistical Computing, 2020).
    Google Scholar 
    Clarke, K. R., Gorley, R., Somerfield, P. & Warwick, R. Change in Marine Communities: an Approach to Statistical Analysis and Interpretation 3rd edn (Prim. Plymouth, 2014).Shannon, C. E. The mathematical theory of communication. MD Comput. https://doi.org/10.2307/410457 (1997).Article 
    PubMed 

    Google Scholar 
    Faith, D. P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. https://doi.org/10.1016/0006-3207(92)91201-3 (1992).Article 

    Google Scholar 
    Bates, D., Mächler, M., Bolker, B. M. & Walker, S. C. Fitting linear mixed-effects models using lme4. J. Stat. Softw. https://doi.org/10.18637/jss.v067.i01 (2015).Article 

    Google Scholar 
    Fox, J. et al. The car Package. R (2012).Zuur, A. F., Ieno, E. N. & Elphick, C. S. A protocol for data exploration to avoid common statistical problems. Methods Ecol. Evol. https://doi.org/10.1111/j.2041-210x.2009.00001.x (2010).Article 

    Google Scholar 
    DHARMa: Residual diagnostics for hierarchical (multi-level/mixed) regression models. https://cran.r-project.org/web/packages/DHARMa/vignettes/DHARMa.html.Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).Book 

    Google Scholar 
    McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE https://doi.org/10.1371/journal.pone.0061217 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B https://doi.org/10.1111/j.2517-6161.1995.tb02031.x (1995).Article 
    MATH 

    Google Scholar 
    Whittaker, R. H. Vegetation of the Siskiyou mountains Oregon and California. Ecol. Monogr. https://doi.org/10.2307/1948435 (1960).Article 

    Google Scholar 
    Paulson, J. metagenomeSeq: Statistical analysis for sparse high-throughput sequencing. Bioconductor.Jp (2014).Bray, J. R. & Curtis, J. T. An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. https://doi.org/10.2307/1942268 (1957).Article 

    Google Scholar 
    Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.01996-06 (2007).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Oksanen, J. et al. Package ‘vegan’ Title Community Ecology Package Version 2.5-6. cran.ism.ac.jp (2019).Anderson, M. J. & Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. https://doi.org/10.1046/j.1442-9993.2001.01070.x (2001).Article 

    Google Scholar 
    Clarke, K. R. & Ainsworth, M. A method of linking multivariate community structure to environmental variables. Mar. Ecol. Prog. Ser. https://doi.org/10.3354/meps092205 (1993).Article 

    Google Scholar 
    QGIS Development Team. QGIS Geographic Information System (Open Source Geospatial Foundation, 2019).
    Google Scholar  More

  • in

    Apparent absence of avian malaria and malaria-like parasites in northern blue-footed boobies breeding on Isla Isabel

    Atkinson, C. T. & Van Riper, C. Pathogenicity and epizootiology of avian haematozoa: Plasmodium, Leucocytozoon, and Haemoproteus. Bird-Parasite Interact. 2, 19–48 (1991).
    Google Scholar 
    Sorci, G. & Moller, A. P. Comparative evidence for a positive correlation between haematozoan prevalence and mortality in waterfowl. J. Evol. Biol. 10, 731–741 (1997).
    Google Scholar 
    Merino, S., Moreno, J., Sanz, J. J. & Arriero, E. Are avian blood parasites pathogenic in the wild? A medication experiment in blue tits (Parus caeruleus). Proc. Biol. Sci. 267, 2507–2510 (2000).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Asghar, M. et al. Hidden costs of infection: Chronic malaria accelerates telomere degradation and senescence in wild birds. Science 347, 436–438 (2015).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Quillfeldt, P., Arriero, E., Martínez, J., Masello, J. F. & Merino, S. Prevalence of blood parasites in seabirds – A review. Front. Zool. 8, 26 (2011).PubMed 
    PubMed Central 

    Google Scholar 
    Piersma, T. Do global patterns of habitat use and migration strategies co-evolve with relative investments in immunocompetence due to spatial variation in parasite pressure?. Oikos 80, 623 (1997).
    Google Scholar 
    Mendes, L., Piersma, T., Lecoq, M., Spaans, B. & Ricklefs, R. E. Disease-limited distributions? Contrasts in the prevalence of avian malaria in shorebird species using marine and freshwater habitats. Oikos 109, 396–404 (2005).
    Google Scholar 
    Martínez-Abraín, A., Esparza, B. & Oro, D. Lack of blood parasites in bird species: Does absence of blood parasite vectors explain it all?. Ardeola 51, 225–232 (2004).
    Google Scholar 
    Campioni, L. et al. Absence of haemosporidian parasite infections in the long-lived Cory’s shearwater: Evidence from molecular analyses and review of the literature. Parasitol. Res. 117, 323–329 (2018).PubMed 

    Google Scholar 
    Osorio-Beristain, M. & Drummond, H. Non-aggressive mate guarding by the blue-footed booby: A balance of female and male control. Behav. Ecol. Sociobiol. 43, 307–315 (1998).
    Google Scholar 
    Nelson, J. B. Pelicans, Cormorants and Their Relatives: The Pelecaniformes (Oxford University Press, 2006).
    Google Scholar 
    Kim, S. Y., Torres, R., Domínguez, C. A. & Drummond, H. Lifetime philopatry in the blue-footed booby: A longitudinal study. Behav. Ecol. 18, 1132–1138 (2007).
    Google Scholar 
    Drummond, H. & Rodríguez, C. Viability of booby offspring is maximized by having one young parent and one old parent. PLoS ONE 10, e0133213 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Lee-Cruz, L. et al. Prevalence of Haemoproteus sp. in Galápagos blue-footed boobies: Effects on health and reproduction. Parasitol. Open 2 (2016).Santiago-Alarcon, D., Palinauskas, V. & Schaefer, H. M. Diptera vectors of avian Haemosporidian parasites: Untangling parasite life cycles and their taxonomy. Biol. Rev. 87, 928–964 (2012).PubMed 

    Google Scholar 
    Bond, J. G. et al. Diversity of mosquitoes and the aquatic insects associated with their oviposition sites along the Pacific coast of Mexico. Parasit. Vectors 7, 41 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    Ibañez-Bernal, S. Informe Final del Proyecto Actualización del Catálogo de Autoridad Taxonómica del Orden Diptera (Insecta) de México CONABIO (JE006). (2017).Levin, I. I. et al. Hippoboscid-transmitted Haemoproteus parasites (Haemosporida) infect Galapagos Pelecaniform birds: Evidence from molecular and morphological studies, with a description of Haemoproteus iwa. Int. J. Parasitol. 41, 1019–1027 (2011).PubMed 

    Google Scholar 
    Madsen, V. et al. Testosterone levels and gular pouch coloration in courting magnificent frigatebird (Fregata magnificens): Variation with age-class, visited status and blood parasite infection. Horm. Behav. 51, 156–163 (2007).CAS 
    PubMed 

    Google Scholar 
    Clark, G. W. & Swinehart, B. Avian haematozoa from the offshore islands of northern Mexico. Wildl. Dis. 5, 111–112 (1969).CAS 
    PubMed 

    Google Scholar 
    Quillfeldt, P. et al. Hemosporidian blood parasites in seabirds—A comparative genetic study of species from Antarctic to tropical habitats. Naturwissenschaften 97, 809–817 (2010).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Merino, S. et al. Infection by haemoproteus parasites in four species of frigatebirds and the description of a new species of Haemoproteus (Haemosporida: Haemoproteidae). J. Parasitol. 98, 388–397 (2012).PubMed 

    Google Scholar 
    Svensson, L. M. E. & Ricklefs, R. E. Low diversity and high intra-island variation in prevalence of avian Haemoproteus parasites on Barbados, Lesser Antilles. Parasitology 136, 1121–1131 (2009).PubMed 

    Google Scholar 
    Loiseau, C. et al. Spatial variation of haemosporidian parasite infection in african rainforest bird species. J. Parasitol. 96, 21–29 (2010).PubMed 

    Google Scholar 
    Madsen, V. Female Mate Choice in the Magnificent Frigatebird (Fregata magnificens) (Universidad Nacional Autónoma de México, 2004).
    Google Scholar 
    Super, P. E. & van Riper, C. A comparison of avian hematozoan epizootiology in two California coastal scrub communities. J. Wildl. Dis. 31, 447–461 (1995).CAS 
    PubMed 

    Google Scholar 
    CONANP. Programa de Conservación y Manejo del Parque Nacional Isla Isabel. (2005).Ancona, S., Drummond, H., Rodríguez, C. & Zúñiga-Vega, J. J. Long-term population dynamics reveal that survival and recruitment of tropical boobies improve after a hurricane. J. Avian Biol. 48, 320–332 (2017).
    Google Scholar 
    Martínez-de la Puente, J., Martinez, J., Rivero-de Aguilar, J., Herrero, J. & Merino, S. On the specificity of avian blood parasites: Revealing specific and generalist relationships between haemosporidians and biting midges. Mol. Ecol. 20, 3275–3287 (2011).PubMed 

    Google Scholar 
    Bastien, M., Jaeger, A., Le Corre, M., Tortosa, P. & Lebarbenchon, C. Haemoproteus iwa in Great Frigatebirds (Fregata minor) in the Islands of the Western Indian Ocean. PLoS ONE 9, e97185 (2014).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Maa, T. C. Records of Hippoboscidae (diptera) from the Central Pacific. J. Med. Ent. 3, 325–328 (1968).
    Google Scholar 
    Levin, I. I. & Parker, P. G. Comparative host–parasite population genetic structures: Obligate fly ectoparasites on Galapagos seabirds. Parasitology 140, 1061–1069 (2013).CAS 
    PubMed 

    Google Scholar 
    Ramos-González, A. Hábitat y Edad de los Bobos de Patas Azules: Factores Importantes Para la Paternidad y Abundancia de Garrapatas. Primera edición. 88. (Universidad Nacional Autónoma de México, 2019). Print ISBN 978-607-30-1489-2.Bensch, S. et al. Contaminations contaminate common databases. Mol. Ecol. Resour. 21, 355–362 (2021).CAS 
    PubMed 

    Google Scholar 
    Taylor, S. A., Maclagan, L., Anderson, D. J. & Friesen, V. L. Could specialization to cold-water upwelling systems influence gene flow and population differentiation in marine organisms? A case study using the blue-footed booby, Sula nebouxii. J. Biogeogr. 38, 883–893 (2011).
    Google Scholar 
    Kalbe, M. & Kurtz, J. Local differences in immunocompetence reflect resistance of sticklebacks against the eye fluke Diplostomum pseudospathaceum. Parasitology 132, 105–116 (2006).CAS 
    PubMed 

    Google Scholar 
    Martin, L. B., Gilliam, J., Han, P., Lee, K. & Wikelski, M. Corticosterone suppresses cutaneous immune function in temperate but not tropical house sparrows Passer domesticus. Gen. Comp. Endocrinol. 140, 126–135 (2005).CAS 

    Google Scholar 
    Becker, D. J. et al. Macroimmunology: The drivers and consequences of spatial patterns in wildlife immune defence. J. Anim. Ecol. 89, 972–995 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    Ting, J. et al. Malaria parasites and related haemosporidians cause mortality in cranes: A study on the parasites diversity, prevalence and distribution in Beijing Zoo. Malar. J. 17, 234 (2018).
    Google Scholar 
    Grilo, M. L. et al. Malaria in penguins – Current perceptions. Avian Pathol. 45, 393–407 (2016).CAS 
    PubMed 

    Google Scholar 
    Jovani, R. & Tella, J. L. Parasite prevalence and sample size: misconceptions and solutions. Trends Parasitol. 22, 214–218 (2006).PubMed 

    Google Scholar 
    Bensch, S. et al. Temporal dynamics and diversity of avian malaria parasites in a single host species. J. Anim. Ecol. 76, 112–122 (2007).MathSciNet 
    PubMed 

    Google Scholar 
    Lachish, S., Knowles, S. C., Alves, R., Wood, M. J. & Sheldon, B. C. Infection dynamics of endemic malaria in a wild bird population: Parasite species-dependent drivers of spatial and temporal variation in transmission rates. J. Anim. Ecol. 80, 1207–1216 (2011).PubMed 

    Google Scholar 
    Lopes, V. L. et al. High fidelity defines the temporal consistency of host-parasite interactions in a tropical coastal ecosystem. Sci. Rep. 10, 16839 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Valkiunas, G. et al. A comparative analysis of microscopy and PCR-based detection methods for blood parasites. J. Parasitol. 94, 1395–1401 (2008).CAS 
    PubMed 

    Google Scholar 
    Santiago-Alarcon, D. et al. Parasites in space and time: A case study of haemosporidian spatiotemporal prevalence in urban birds. Int. J. Parasitol. 49, 235–246 (2019).PubMed 

    Google Scholar 
    Ancona, S., Sánchez-Colón, S., Rodríguez, C. & Drummond, H. E. Niño in the warm tropics: Local sea temperature predicts breeding parameters and growth of blue-footed boobies. J. Anim. Ecol. 80, 799–808 (2011).PubMed 

    Google Scholar 
    Drummond, H., Torres, R. & Krishnan, V. V. Buffered development: Resilience after aggressive subordination in infancy. Am. Nat. 161, 794–807 (2003).PubMed 

    Google Scholar 
    Merino, S. & Potti, J. High prevalence of hematozoa in nestlings of a passerine species, the pied flycatcher (Ficedula hypoleuca). Auk 112, 1041–1043 (1995).
    Google Scholar 
    Gutiérrez-López, R. et al. Low prevalence of blood parasites in a long-distance migratory raptor: The importance of host habitat. Parasit. Vectors 8, 189 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    Hellgren, O., Waldenström, J. & Bensch, S. A new PCR assay for simultaneous studies of Leucocytozoon, Plasmodium, and Haemoproteus from avian blood. J. Parasitol. 90, 797–802 (2004).CAS 
    PubMed 

    Google Scholar 
    Bensch, S. et al. Host specificity in avian blood parasites: A study of Plasmodium and Haemoproteus mitochondrial DNA amplified from birds. Proc. Biol. Sci. 267, 1583–1589 (2000).CAS 
    PubMed 
    PubMed Central 

    Google Scholar  More