More stories

  • in

    Influence of suspended inorganic particles (kaolinite) on eggs and larvae of the pelagic shrimp Lucensosergia lucens

    Uchida, H. & Baba, O. Fishery management and the pooling arrangement in the Sakura ebi fishery in Japan, 175–189. https://www.fao.org/3/a1497e/a1497e16.pdf (2008).Omori, M. The biology of a sergestid shrimp Sergestes lucens Hansen. Bull. Ocean Res. Inst. Univ. Tokyo 4, 1–83 (1969).
    Google Scholar 
    Gurney, R. & Lebour, M. V. Larvae of decapod crustacea. Part VI. The genus Sergestes. Discov. Rep. 20, 1–68 (1940).
    Google Scholar 
    Holthuis, L. B. FAO species catalogue. Vol. 1. Shrimps and prawns of the world. An annotated catalogue of species of interest to fisheries. FAO Fish. Synop. Vol. 125, 1–271 (1980).Omori, M., Ukishima, Y. & Muranaka, F. New record of occurrence of Sergia lucens (Hansen) (Crustacea, Sergestidae) off Tung-kang, Taiwan, with special reference to phylogeny and distribution of the species. J. Oceanogr. Soc. Jpn. 44, 261–267 (1988) (in Japanese with English abstract).Article 

    Google Scholar 
    Isshiki, T. & Tajima, Y. The research of a sergestid shrimp, Sergia lucens (Hansen) in the mouth of Tokyo Bay I. The seasonal distribution of adult and the distribution of eggs. Bull. Kanagawa Pref. Fish. Exp. Stn. 13, 73–78 (1992) (in Japanese with English abstract).
    Google Scholar 
    Lee, D. A., Wu, S. H., Liao, I. C. & Yu, H. P. On three species of commercially important sergestid shrimps (Decapoda: Sergestidae) in the coastal waters of Taiwan. J. Taiwan Fish. Res. Inst. 4, 1–19 (1996) (in Chinese with English abstract).CAS 

    Google Scholar 
    Yinji, L. & Ratana, C. Governing in an uncertain time: The case of Sakura shrimp fishery, Japan. Marit. Stud. 20, 115–126 (2021).Article 

    Google Scholar 
    Isono, R. S., Kita, J. & Setoguma, T. Acute effects of kaolinite suspension on eggs and larvae of some marine teleosts. Comp. Biochem. Physiol. Part C 120, 449–455 (1998).CAS 
    Article 

    Google Scholar 
    Aoki, S. & Oinuma, K. Distribution of clay minerals in surface sediments of Suruga Bay, central Japan. J. Geol. Soc. Jpn. 87(7), 429–438 (1981) (in Japanese with English abstract).Article 

    Google Scholar 
    Nasnodkar, M. R. & Ganapati, N. N. Clay mineralogy and chemistry of mudflat core sediments from Sharavathi and Gurupur estuaries: Source and processes. Indian J. Geo-Mar. Sci. 48(3), 379–388 (2019).
    Google Scholar 
    Capper, N. The effects of suspended sediment on the aquatic organisms Daphnia magna and Pimephales promelas. All Theses. 2. https://tigerprints.clemson.edu/all_theses/2 (2006).Boyd, M. B. et al. Disposal of dredge spoil, problem identification and assessment and research program development. Technical report H-72–8, U.S. army engineer waterways experiment station, CE, Vicksburg, Miss. (1972).McFarland, V. A. & Peddicord, R. K. Lethality of a suspended clay to a diverse selection of marine and estuarine macrofauna. Arch. Environ. Contam. Toxicol. 9, 733–741 (1980).CAS 
    Article 

    Google Scholar 
    Arakawa, H. et al. The influence of suspended particles on larval development in the Manila clam Ruditapes philippinarum. Sci. Postp. 1, e00028. https://doi.org/10.14340/spp.2014.08A0002 (2014).Article 

    Google Scholar 
    Davis, H. C. Effects of turbidity-producing materials in sea water on eggs and larvae of the clam (Venus (Mercenaria) mercenaria). Biol. Bull. 118, 48–54 (1960).Article 

    Google Scholar 
    Tabata, A., Morinaga, T. & Arakawa, H. Influences of concentration, particle-size and kind of inorganic suspended matter on feed caught by Manila clam, Ruditapes philippinarum. La Mer 37, 163–171 (2000).CAS 

    Google Scholar 
    Annisa, Dwiatmoko, M. U., Saismana, U. & Maulanai, R. Characteristics of kaolin clay on Alluvial formation subdistrict mataraman based on physical properties and chemical properties. In MATEC Web of Conferences Vol. 280, 03009. https://doi.org/10.1051/matecconf/201928003009 (2019).Murray, H. H. Structure and composition of clay minerals and their physical and chemical properties. Dev. Clay Sci. 2, 7–31. https://doi.org/10.1016/S1572-4352(06)02002-2 (2006).Article 

    Google Scholar 
    Kumari, N. & Mohan, C. Basics of clay minerals and their characteristic properties. Clay Clay Miner. 1–29 (2021).Lively, J. S., Kaufman, Z. & Carpenter, E. J. Phytoplankton ecology of a barrier island estuary: Great South Bay, New York. Estuar. Coast. Shelf Sci. 16(1), 51–68 (1983).ADS 
    Article 

    Google Scholar 
    Lloyd, D. S. Turbidity as a water quality standard for salmonid habitats in Alaska. N. Am. J. Fish. Manag. 7, 34–45 (1987).Article 

    Google Scholar 
    Kirk, K. L. Effects of suspended clay on Daphnia body growth and fitness. Freshw. Biol. 28, 103–109 (1992).Article 

    Google Scholar 
    McCabe, G. D. & O’Brien, W. J. The effects of suspended silt on feeding and reproduction of Daphnia pulex. Am. Midl. Nat. 110, 324–337 (1983).Article 

    Google Scholar 
    Kirk, K. L. & Gilbert, J. J. Suspended clay and the population dynamics of planktonic Rotifers and Cladocerans. Ecology 71, 1741–1755 (1990).Article 

    Google Scholar 
    Loosanoff, V. L. Effects of turbidity on some larval and adult bivalves. Proc. Gulf. Carib. Fish. Inst. 14, 80–95 (1961).
    Google Scholar 
    Arruda, J. A., Marzolf, G. R. & Faulk, R. T. The role of suspended sediments in the nutrition of zooplankton in turbid reservoirs. Ecology 64, 1225–1235 (1983).Article 

    Google Scholar 
    Kathyayani, S. A., Muralidhar, M., Kumar, T. S. & Alavandi, S. V. Stress quantification in Penaeus vannamei exposed to varying levels of turbidity. J. Coast. Res. 86, 177–183 (2019).CAS 
    Article 

    Google Scholar 
    Wilber, D. H. & Clarke, D. G. Biological effects of suspended sediments: A review of suspended sediment impacts on fish and shellfish with relation to dredging activities in estuaries. N. Am. J. Fish. Manag. 21, 855–875 (2001).Article 

    Google Scholar 
    Lin, H., Charmantier, G., Thuet, P. & Trilles, J. Effects of turbidity on survival, osmoregulation, and gill Na+-K+ ATPase in juvenile shrimp Penaeus japonicus. Mar. Ecol. Prog. Ser. 90, 31–37 (1992).ADS 
    CAS 
    Article 

    Google Scholar 
    Davis, H. C. & Hidu, H. Effects of turbidity-producing substances in sea water on eggs and larvae of three genera of bivalve mollusks. Veliger 11, 316–323 (1969).
    Google Scholar 
    Nimmo, D. R., Hamaker, T. L., Matthews, E. & Young, W. T. The long-term effects of suspended particulates on survival and reproduction of the mysid shrimp, Mysidopsis bahia, in the laboratory. In Proceedings of a Symposium on the Ecological Effects of Environmental Stress, New York, 413–422 (1979).Peddicord, R. & McFarland, V. Effects of suspended dredged material on the commercial crab, Cancer magister. In Proceedings of the Specialty Conference on Dredging and Its Environmental Effects, Mobile, Alabama, 633–644 (1976).Peddicord, R. K. Direct Effects of Suspended Sediments on Aquatic Organisms. Contaminants and Sediments. Volume 1. Fate and Transport, Case Studies, Modeling, Toxicity 501–536 (Ann Arbor Science Publishers, 1980).
    Google Scholar 
    Wakeman, T., Peddicord, R. & Sustar, J. Effects of suspended solids associated with dredging operations on estuarine organisms. In Ocean 75 conference, 431–436 (1975).Gebauer, P., Walter, I. & Anger, K. Effects of substratum and conspecific adults on the metamorphosis of Chasmagnathus granulata (Dana) (Decapoda: Grapsidae) megalopae. J. Exp. Mar. Biol. Ecol. 223, 185–198 (1998).Article 

    Google Scholar 
    Carvalho, L. & Calado, R. Trade-offs between timing of metamorphosis and grow out performance of a marine caridean shrimp juveniles and its relevance for aquaculture. Aquaculture 492, 97–102 (2018).Article 

    Google Scholar 
    Calado, R. et al. The physiological consequences of delaying metamorphosis in the marine ornamental shrimp Lysmata seticaudata and its implications for aquaculture. Aquaculture 546, 737391. https://doi.org/10.1016/j.aquaculture.2021.737391 (2022).Article 

    Google Scholar 
    Murphy, R. C. Factors affecting the distribution of the introduced bivalve, Mercenaria mercenaria, in a California lagoon—The importance of bioturbation. J. Mar. Res. 43, 673–692 (1985).Article 

    Google Scholar 
    Bricelj, V. M. & Malouf, R. E. Influence of algal and suspended sediment concentration on the feeding physiology of the hard clam Mercenaria mercenaria. Mar. Biol. 84, 155–165 (1984).Article 

    Google Scholar 
    Wenger, A. S., Jacob, J. L. & Jones, G. P. Increasing suspended sediment reduces foraging, growth, and condition of a planktivorous damselfish. J. Exp. Mar. Biol. Ecol. 428, 43–48 (2012).Article 

    Google Scholar 
    Robinson, W. E., Wehling, W. E. & Morse, M. P. The effect of suspended clay on feeding and digestive efficiency of the surf clam Spisula solidissima (Dillwyn). J. Exp. Mar. Biol. Ecol. 74, 1–12 (1984).CAS 
    Article 

    Google Scholar 
    Turner, E. J. & Miller, D. C. Behavior and growth of Mercenaria mercenaria during simulated storm events. Mar. Biol. 111, 55–64 (1991).Article 

    Google Scholar 
    Grant, J. & Thorpe, B. Effects of suspended sediment on growth, respiration, and excretion of the soft-shelled clam (Mya arenaria). Can. J. Fish. Aquat. Sci. 48, 1285–1292 (1991).Article 

    Google Scholar 
    Gleason, R. A., Euliss, N. H., Hubbard, D. E. & Duffy, W. G. Effects of sediment load on emergence of aquatic invertebrates and plants from wetland soil egg and seed banks. Wetlands 23, 26–34 (2003).Article 

    Google Scholar 
    Jacek, R., Anna, S. & Miroslaw, S. The effect of lake sediment on the hatching success of Daphnia ephippial eggs. J. Limnol. 75, 597–605 (2016).
    Google Scholar 
    Newcombe, C. P. & McDonald, D. D. Effects of suspended sediment on aquatic ecosystems. N. Am. J. Fish. Manag. 11, 77–82 (1991).Article 

    Google Scholar 
    Chutter, F. M. The effects of silt and sand on the invertebrate fauna of streams and rivers. Hydrobiologia 34, 57–76 (1968).Article 

    Google Scholar 
    Hellawell, J. M. Biological indicators of freshwater pollution and environmental management. In Pollution Monitoring Series (ed. Melanby, K.) https://doi.org/10.1007/978-94-009-4315-5 (1986).Makita, M. & Kondo, M. Rearing of the larvae of Seigia Lucens (Hansen). Bull. Shizuoka Pref. Fish. Exp. Stn. 16, 97–105 (1982) (in Japanese).
    Google Scholar  More

  • in

    Biophysical and economic constraints on China’s natural climate solutions

    This study presents a comprehensive quantification of carbon sequestration as well as CO2/CH4/N2O emissions reductions from terrestrial ecosystems based on multiple sources of data from literature, inventories, public databases and documents. The pathways considered ecosystem restoration and protection from being converted into cropland or built-up areas, reforestation, management with improved nitrogen use in cropland, restricted deforestation, grassland recovery, reducing risk from forest wildfire and others. Here we describe the cross-cutting methods that apply across all 16 NCS pathways. The definitions, detailed methods and data sources for evaluating individual pathways can be found in the Supplementary Information.Cross-cutting methodsBaseline settingWe set 2000 as the base year because the large-scale national ecological projects, such as the Grain for Green Project, were started since then. We first evaluate the historical mitigation capacity during 2000–2020, which is the first 20 years of implementing the projects. From this procedure we can determine how much mitigation capacity has been realized through the previous projects in the past two decades and to what extent additional actions can be made after 2020. Relative to the baseline 2000–2020, we then evaluate the maximum potentials of the NCS mitigation in the future 10 (2020–2030) and 40 (2020–2060) years, corresponding to the timetable of China’s NDCs: carbon peak before 2030 and carbon neutrality by 2060.The settings of baseline in this study are different from the existing assessments (2000s–2010s as a baseline and 2010–2025/2030/2050 as scenarios)1,22,23,27,28. Baseline sets the temporal and spatial reference for NCS pathway scenarios, which may have a great impact on the NCS estimates. Notably, NCS actions during 2000–2020 will have a great impact in the future periods, which we refer to as the ‘legacy effect’. The legacy effect itself, mainly reforestation, is independent of being assessed, but it is conceptually attributed to natural flux and excluded from future NCS potential estimates.Maximum potentialThe MAMP refers to the additional CO2 sequestration or avoided GHG emissions measured in CO2 equivalents (CO2e) at given flux rates in a period on the maximum extent to which the stewardship options are applied (numbers are expressed as TgCO2e yr−1 for individual pathways and PgCO2e yr−1 for national total) (Extended Data Fig. 1 and Supplementary Table 2). ‘Additional’ means mitigation outcomes due to human actions taken beyond business-as-usual land-use activities (since 2020) and excluding existing land fluxes not attributed to direct human activities1. The MAMP of CH4 and N2O are accounted by three cropland and wetland pathways (cropland nutrient management, improved rice cultivation and peatland restoration). We adopt 100 yr global warming potential to calculate the warming equivalent for CH4 (25) and N2O (298), respectively38,39 because these values are used in national GHG inventories, although some researchers have argued that using the fixed 100 yr global warming potential to calculate the warming equivalents may be problematic because they cannot differentiate the contrasting impacts of the long- and short-lived climate pollutants39. Because the flux rate of the GHG by ecosystems may vary with the time of recovery or growth, the MAMP may also change for different periods even given the same extent.The ‘maximum’ is constrained by varied factors across the NCS pathways. We constrain forest and grassland restoration by the rate of implementation, farmland red line and tree surviving rate (Extended Data Fig. 2). Surviving rate here is the ratio of the area with increased vegetation cover due to reforestation to the total reforestation area. The farmland red line refers to ‘the minimum area of cultivated land’ given by the Ministry of Land and Resources of China. It defines the lowest limit, and the current red line is ~120 Mha. It is a rigid constraint below which the total amount of cultivated land cannot be reduced. From this total amount, there is provincial farmland red line. This red line sets a constraint on the implementation of the NCS pathways associated with land-use change. We set the future scenario of farmland area that can be used for grassland or forest restoration on the basis of the provincial farmland red line. Basic farmland is closely related to national food security. By 2050, China’s population is predicted to decrease slightly, but with economic development, the per capita demand for food may increase40. We assume that the food production in the future can meet the food demand via increasing agricultural investment and technological advancement. The N fertilizer reduction scenario is set to be below the level 60%, under which crop yield is not significantly affected19, because N fertilizer is surplus in many Chinese croplands. For timber production, we assume that the demand for timber can be met if the production level is maintained at the level of 2010–2020 (83.31 million m3 yr−1). As deforestation of natural forests is 100% forbidden since 2020, the future timber will come mainly from tree plantations. For grazing optimization, we assume that livestock production is not affected by grassland fencing due to refined livestock management such as improving feed nutrient and fine-seed breeding41.The areas of historical NCS implementation during 2000–2020 were estimated using statistical data, published literature and public documents, with a supplement from remote-sensing data. The flux rates were obtained either by directly using the values from multiple literature sources or from estimates using the empirical formulae. For the estimates of future NCS potential, the flux rate and extent of the pathway were determined on the basis of the baseline (2000–2020). The extent is assumed to be achieved by using the same rate but limited by the multiple constraints stated in the preceding unless the implementation scopes have been reported in national planning documents. We estimate the legacy effect by multiplying the implementation area in the past by the flux rates in the future two periods.SaturationThe future mitigation potential that we estimate for 2030 and 2060 will not persist indefinitely because the finite potential for natural ecosystems to store additional carbon will saturate. For each NCS pathway, we estimate the expected duration of the potential for sequestration at the maximum rate (Supplementary Table 3). Forests can continue to sequester carbon for 70–100 years or more. Restored grasslands and fenced grasslands can continue to sequester carbon for >50 years. Forest-fire management and cover crops can continue to sequester carbon for 40–50 years or more. Sea grasses and peatlands can continue to sequester carbon for millennia. Avoided pathways do not saturate as long as the business-as-usual cases indicate that there are potential areas for avoided losses of ecosystems. In this case, sea grass and salt marsh would disappear entirely after 64 years, but it would be 100–300 years or more for forest, grassland and peatland.Estimation of uncertaintiesThe extent (area or biomass amount) and flux (sequestration or reduced emission per area or biomass amount in unit time) are considered to estimate uncertainty of the historical mitigation capacity or future potential for each NCS pathway. We use the IPCC approaches to combine uncertainty42. Where mean and standard deviation can be estimated from collected literature, 95% CIs are presented on the basis of multiple published estimates. Where a sample of estimates is not available but only a range of a factor, we report uncertainty as a range and use Monte Carlo simulations (with normal distribution and 100,000 iterations) to combine the uncertainties of extent and flux (IPCC Approach 2). The overall uncertainties of the 16 NCS pathways were combined using IPCC Approach 142. If the extent estimate is based on a policy determination, rather than an empirical estimate of biophysical potential, we do not consider it a source of uncertainty.MACsThe economic/cost constraints refer to the amount of NCS that can be achieved at a given social cost. The MAC curve is fitted according to the total publicly funded investment and total mitigation capacity or potential during a period. The MAC curves are drawn to estimate the historical mitigation or MAMP at the cost thresholds of US$10, US$50 and US$100 (MgCO2e)−1, respectively. The trading price in China’s current carbon market is ~US$10 USD (as the minimum cost43), and the cost-effective price point44,45 to achieve the Paris Agreement goal of limiting global warming to below 2 °C above pre-industrial levels is US$100 (as the maximum cost). A carbon price of US$50 is regarded as a medium value1,46. For the pathways of reforestation, avoided grassland conversion, grazing optimization and grassland restoration, we collected the statistical data of investments in China from 2000 to 2020 and estimated the affordable MAMP below the three mitigation costs. Due to data limitations, the points used for fitting the MAC curve are values for cost (invested funds) and benefit (mitigation capacity) in each of the provinces. We rank the ratio of benefit to cost in a descending order to obtain the maximum marginal benefit for MAC by assuming that NCS measures are first implemented in the region with the highest cost/benefit rate. We refer to the investment standard before 2020 as the benchmark and estimate the cost of each pathway for the future periods with discount rates of 3% and 5%, respectively. The social discount rate 4–6% is usually used as a benchmark discount value in carbon price studies in China compared with lower scenarios (for example, 3.6%)46,47. In a global study for estimating country-level social cost of carbon, 3% and 5% are used for scenario analysis48. Note that the mean value from the two discount rates was used in presenting the results. For the other pathways where investment data cannot be obtained, we refer to relevant references to estimate MAC. All the cost estimates are expressed in 2015 dollars, transformed on the basis of the Renminbi and US dollar exchange rate of the same year. The year 2015 represents a relatively stable condition of economic increase over the past decade (2011–2020) in China (the increase rate of gross domestic product (GDP) in 2015 is similar to the 10 yr mean). In the cases when the MAC curves exceed the estimated maximum potentials in the period, we identify the historical capacity or the MAMP as limited by the biophysical estimates.Additional mitigation required to meet Paris Agreement NDCsOn 28 October 2021, China officially submitted ‘China’s Achievements, New Goals and New Measures for Nationally Determined Contributions’ (‘New Measures 2021’ hereafter) and ‘China’s Mid-Century Long-Term Low Greenhouse Gas Emission Development Strategy’ to the Secretariat of the United Nations Framework Convention on Climate Change as an enhanced strategy to China’s updated NDCs (first submission in 2015). The goal of China’s updated NDCs is to strive to peak CO2 emissions before 2030 and achieve carbon neutralization by 2060. It specified the goals to include the following: before 2030, China’s carbon dioxide emissions per unit of GDP are expected be more than 65% lower than that in 2005, and the forest stock volume is expected to be increased by around 6.0 (previously 4.5) billion m3 over the 2005 level. In the ‘New Measures 2021’9 and ‘Master Plan of Major Projects of National Important Ecosystem Protection and Restoration (2021–2035)’5, many NCS-related opportunities are proposed to consolidate the carbon sequestration of ecosystems and increase the future NCS potential, including protecting the existing ecosystems, implementing engineering to precisely improve forest quality, continuously increasing forest area and stock volume, strengthening grassland protection and recovery and wetland protection and improving the quality of cultivated land and the agricultural carbon sinks.Industrial CO2 emissionsThe historical CO2 emissions data from 2000 to 201749,50 are used as the benchmark of industrial CO2 emissions during 2000–2020. For future projections, we use the peak value of the A1B2C2 scenario (in the range of 10,000 to 12,000 Mt) in 2030 from ref. 11. We assume that CO2 emission increases linearly from 2017 to 2030.Characterizing co-benefitsNCS activities proposed in the future measures or plans may enhance co-benefits. Four generalized types of ecosystem services are identified: improving biodiversity, water-related, soil-related and air-related ecosystem services (Fig. 1). Biodiversity benefits refer to the increase in different levels of diversity (alpha, beta and/or gamma diversity)51. Water, soil and air benefits refer to flood regulation and water purification, improved fertility and erosion prevention, and improvements in air quality, respectively, as defined in the Millennium Ecosystem Assessment52. The evidence that each pathway produces co-benefits from one or more peer-reviewed publications was collected through reviewing the literature (see the details for co-benefits of each pathway in Supplementary Information).Mapping province-level mitigationThe data for extent of implementing forest pathways are obtained from the statistical yearbook and reported at the province level. To be consistent with the forest pathways, the other pathways were also aggregated to the provincial-level estimate from the spatial data. If the flux data were available in different climate regions, the provinces are first assigned to climate regions. When a province spans multiple climate zones, the weight value is set according to the proportion of area, and finally an estimated value of rate was calculated (for fire management, some grassland and wetland pathways). For the forest pathways, we first collected the flux-rate data from reviewing literature and then averaged these flux rates to region/province. The flux rates for reforestation and natural forest management were calculated separately by province and age group. Similarly, specified flux rates are applied for different times after ecosystem restoration or conversion for other pathways.Classification of NCS typesThree types of NCS pathways were classified: protection (of intact natural ecosystems), improved management (on managed lands) and restoration (of native cover)35. In our study, four (AVFC, AVGC, AVCI, AVPI), eight (IMP, NFM, FM, BIOC, CVCR, CRNM, IMRC, GROP) and four (RF, GRR, CWR, PTR) NCS pathways were identified as protection, management and restoration types, respectively (Supplementary Table 1). These pathways can be further divided into groups of ‘single’ type or ‘mixed’ type according to their contribution to individual pathways. Specifically, in a certain area, when the mitigation capacity of a certain pathway accounts for more than 50% of the total, it is regarded as a single or dominant NCS type; if no single pathway accounts for more than 50%, it is a mixed type, named by the top pathways whose NCS sum exceeds 50% of the total mitigation capacity. More

  • in

    Mount Everest’s harsh heights shelter a rich array of life

    Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
    the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
    Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
    and JavaScript. More

  • in

    Ecoenzymatic stoichiometry reveals widespread soil phosphorus limitation to microbial metabolism across Chinese forests

    Bastin, J. F. et al. The global tree restoration potential. Science 364, 76–79 (2019).Article 
    CAS 

    Google Scholar 
    Lewis, S. L., Wheeler, C. E., Mitchard, E. T. A. & Koch, A. Restoring natural forests is the best way to remove atmospheric carbon. Nature 568, 25–28 (2019).CAS 
    Article 

    Google Scholar 
    Bonan, G. B. Forests and climate change: forcings, feedbacks, and the climate benefits of forests. Science 320, 1444–1449 (2008).CAS 
    Article 

    Google Scholar 
    Beer, C. et al. Terrestrial gross carbon dioxide uptake: global distribution and covariation with climate. Science 329, 834–838 (2010).CAS 
    Article 

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

    Google Scholar 
    Camenzind, T., Httenschwiler, S., Treseder, K. K., Lehmann, A. & Rillig, M. C. Nutrient limitation of soil microbial processes in tropical forests. Ecol. Monogr. 88, 4–21 (2018).Article 

    Google Scholar 
    Hou, E., Luo, Y., Kuang, Y., Chen, C. & Wen, D. Global meta-analysis shows pervasive phosphorus limitation of aboveground plant production in natural terrestrial ecosystems. Nat. Commun. 11, 1–9 (2020).Article 
    CAS 

    Google Scholar 
    Du, E. et al. Global patterns of terrestrial nitrogen and phosphorus limitation. Nat. Geosci. 13, 221–226 (2020).CAS 
    Article 

    Google Scholar 
    Sinsabaugh, R. L. & Follstad Shah, J. J. Ecoenzymatic stoichiometry and ecological theory. Annu. Rev. Ecol. Evol. Syst. 43, 313–343 (2012).Article 

    Google Scholar 
    Houghton, R. A. Balancing the global carbon budget. Annu. Rev. Earth Planet. Sci. 35, 313–347 (2007).CAS 
    Article 

    Google Scholar 
    Chen, J. et al. Differential responses of carbon-degrading enzyme activities to warming: implications for soil respiration. Global Change Biol. 24, 4816–4826 (2018).Article 

    Google Scholar 
    Waring, B. G., Weintraub, S. R. & Sinsabaugh, R. L. Ecoenzymatic stoichiometry of microbial nutrient acquisition in tropical soils. Biogeochemistry 117, 101–113 (2014).CAS 
    Article 

    Google Scholar 
    Mori, T., Lu, X., Aoyagi, R. & Mo, J. Reconsidering the phosphorus limitation of soil microbial activity in tropical forests. Funct. Ecol. 32, 1145–1154 (2018).Article 

    Google Scholar 
    Gallardo, A. & Schlesinger, W. H. Factors limiting microbial biomass in the mineral soil and forest floor of a warm-temperate forest. Soil Biol. Biochem. 26, 1409–1415 (1994).Article 

    Google Scholar 
    Feng, J. et al. Coupling and decoupling of soil carbon and nutrient cycles across an aridity gradient in the drylands of northern China: Evidence from ecoenzymatic stoichiometry. Global Biogeochem. Cycles. 33, 559–569 (2019).CAS 

    Google Scholar 
    Cui, Y. et al. Patterns of soil microbial nutrient limitations and their roles in the variation of soil organic carbon across a precipitation gradient in an arid and semi-arid region. Sci. Total Environ. 658, 1440–1451 (2019).CAS 
    Article 

    Google Scholar 
    Jing, X. et al. Soil microbial carbon and nutrient constraints are driven more by climate and soil physicochemical properties than by nutrient addition in forest ecosystems. Soil Biol. Biochem. 141, 107657 (2020).CAS 
    Article 

    Google Scholar 
    Fernández-Martínez, M. et al. Nutrient availability as the key regulator of global forest carbon balance. Nat. Clim. Change 4, 471–476 (2014).Article 
    CAS 

    Google Scholar 
    Zhou, L. et al. Soil extracellular enzyme activity and stoichiometry in China’s forests. Funct. Ecol. 34, 1461–1471 (2020).Article 

    Google Scholar 
    Fang, J., Chen, A., Peng, C., Zhao, S. & Ci, L. Changes in forest biomass carbon storage in China between 1949 and 1998. Science 292, 2320–2322 (2001).CAS 
    Article 

    Google Scholar 
    Zhu, J. et al. Carbon stocks and changes of dead organic matter in China’s forests. Nat. Commun. 8, 1–10 (2017).Article 
    CAS 

    Google Scholar 
    Fang, J., Yu, G., Liu, L., Hu, S. & Chapin, F. S. Climate change, human impacts, and carbon sequestration in China. Proc. Natl. Acad. Sci. USA 115, 4015–4020 (2018).CAS 
    Article 

    Google Scholar 
    Sinsabaugh, R. L. et al. Stoichiometry of soil enzyme activity at global scale. Ecol. Lett. 11, 1252–1264 (2008).Article 

    Google Scholar 
    Sinsabaugh, R. L., Hill, B. H. & Follstad Shah, J. J. Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment. Nature 462, 795–798 (2009).CAS 
    Article 

    Google Scholar 
    Moorhead, D. L., Sinsabaugh, R. L., Hill, B. H. & Weintraub, M. N. Vector analysis of ecoenzyme activities reveal constraints on coupled C, N and P dynamics. Soil Biol. Biochem. 93, 1–7 (2016).CAS 
    Article 

    Google Scholar 
    Cui, Y. et al. Stoichiometric models of microbial metabolic limitation in soil systems. Global Ecol. Biogeogr. 30, 2297–2311 (2021).Article 

    Google Scholar 
    Elser, J. J. et al. Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine, and terrestrial ecosystems. Ecol. Lett. 10, 1135–1142 (2007).Article 

    Google Scholar 
    Schulte-Uebbing, L. & Vries, W. D. Global-scale impacts of nitrogen deposition on tree carbon sequestration in tropical, temperate, and boreal forests: a meta-analysis. Global Change Biol. 24, 416–431 (2017).Article 

    Google Scholar 
    Richardson, S. J., Peltzer, D. A., Allen, R. B. & Parfitt, M. G. L. Rapid development of phosphorus limitation in temperate rainforest along the Franz josef soil chronosequence. Oecologia 139, 267–276 (2004).Article 

    Google Scholar 
    Augusto, L., Achat, D. L., Jonard, M., Vidal, D. & Ringeval, B. Soil parent material-a major driver of plant nutrient limitations in terrestrial ecosystems. Global Change Biol. 23, 3808–3824 (2017).Article 

    Google Scholar 
    Yao, Q. et al. Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nat. Ecol. Evol. 2, 499–509 (2018).Article 

    Google Scholar 
    Philippot, L., Raaijmakers, J. M., Lemanceau, P. & Putten, W. H. Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11, 789–799 (2013).CAS 
    Article 

    Google Scholar 
    Kuzyakov, Y. & Xu, X. Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance. New Phytol. 198, 656–669 (2013).CAS 
    Article 

    Google Scholar 
    Cui, Y. et al. Ecoenzymatic stoichiometry and microbial nutrient limitation in rhizosphere soil in the arid area of the northern Loess Plateau, China. Soil Biol. Biochem. 116, 11–21 (2018).CAS 
    Article 

    Google Scholar 
    Cui, Y. et al. Soil moisture mediates microbial carbon and phosphorus metabolism during vegetation succession in a semiarid region. Soil Biol. Biochem. 147, 107814 (2020).CAS 
    Article 

    Google Scholar 
    Johnson, J. et al. The response of soil solution chemistry in european forests to decreasing acid deposition. Global Change Biol. 24, 3603–3619 (2018).Article 

    Google Scholar 
    Janssens, I. A. et al. Reduction of forest soil respiration in response to nitrogen deposition. Nat. Geosci. 3, 315–322 (2010).CAS 
    Article 

    Google Scholar 
    Penuelas, J. et al. Human-induced nitrogen-phosphorus imbalances alter natural and managed ecosystems across the globe. Nat. Commun. 4, 1–10 (2013).
    Google Scholar 
    Yu, G. et al. Stabilization of atmospheric nitrogen deposition in china over the past decade. Nat. Geosci. 12, 424–429 (2019).CAS 
    Article 

    Google Scholar 
    Cui, Y. et al. Decreasing microbial phosphorus limitation increases soil carbon release. Geoderma 419, 115868 (2022).CAS 
    Article 

    Google Scholar 
    Sinsabaugh, R. L., Moorhead, D. L., Xu, X. & Litvak, M. E. Plant, microbial and ecosystem carbon use efficiencies interact to stabilize microbial growth as a fraction of gross primary production. New Phytol. 214, 1518–1526 (2017).CAS 
    Article 

    Google Scholar 
    Craig, M. E., Mayes, M. A., Sulman, B. N. & Walker, A. P. Biological mechanisms may contribute to soil carbon saturation patterns. Global Change Biol. 27, 2633–2644 (2021).CAS 
    Article 

    Google Scholar 
    Friggens, N. L., Hester, A. J., Mitchell, R. J., Parker, T. C. & Wookey, P. A. Tree planting in organic soils does not result in net carbon sequestration on decadal timescales. Global Change Biol. 26, 5178–5188 (2020).Article 

    Google Scholar 
    Jiang, M. et al. The fate of carbon in a mature forest under carbon dioxide enrichment. Nature 580, 227–231 (2020).CAS 
    Article 

    Google Scholar 
    Rosinger, C., Rousk, J. & Sandén, H. Can enzymatic stoichiometry be used to determine growth-limiting nutrients for microorganisms?-A critical assessment in two subtropical soils. Soil Biol. Biochem. 128, 115–126 (2019).CAS 
    Article 

    Google Scholar 
    Mori, T. Does ecoenzymatic stoichiometry really determine microbial nutrient limitations? Soil Biol. Biochem. 146, 107816 (2020).CAS 
    Article 

    Google Scholar 
    Allison, S. D., Wallenstein, M. D. & Bradford, M. A. Soil-carbon response to warming dependent on microbial physiology. Nat. Geosci. 3, 336–340 (2010).CAS 
    Article 

    Google Scholar 
    Saiya-Cork, K. R., Sinsabaugh, R. L. & Zak, D. R. The effects of long term nitrogen deposition on extracellular enzyme activity in an acer saccharum, forest soil. Soil Biol. Biochem. 34, 1309–1315 (2002).CAS 
    Article 

    Google Scholar 
    German, D. P. et al. Optimization of hydrolytic and oxidative enzyme methods for ecosystem studies. Soil Biol. Biochem. 43, 1387–1397 (2011).CAS 
    Article 

    Google Scholar 
    Lindstrom, M. J. & Bates, D. M. Newton-Raphson and EM Algorithms for Linear Mixed-Effects Models for Repeated-Measures Data. J. Am. Stat. Assoc. 83, 1014–1022 (1988).
    Google Scholar 
    Legendre, P. & Legendre, L. Numerical ecology, 2nd English edition. Elsevier Science BV, Amsterdam (1998).Muggeo, V. M. R. Segmented: an R package to fit regression models with broken-line relationships. R News 8/1, 20–25 (2008).
    Google Scholar 
    Toms, J. D. & Lesperance, M. Piecewise regression: a tool for identifying ecological thresholds. Ecology 84, 2034–2041 (2003).Article 

    Google Scholar 
    Borcard, D., Legendre, P. & Drapeau, P. Partialling out the spatial component of ecological variation. Ecology 73, 1045–1055 (1992).Article 

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

    Google Scholar 
    Sanchez, G., Trinchera, L. & Russolillo, G. plspm: Tools for Partial Least Squares Path Modeling (PLS-PM). R package version 0.4.7 edn (2016).Development Core Team R. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2016). More

  • in

    Cell death responses to acute high light mediated by non-photochemical quenching in the dinoflagellate Karenia brevis

    Brand, L. E., Campbell, L. & Bresnan, E. Karenia: The biology and ecology of a toxic genus. Harmful Algae 14, 156–178 (2012).
    Google Scholar 
    Hetland, R. D. & Campbell, L. Convergent blooms of Karenia brevis along the Texas coast. Geophys. Res. Lett. 34, 1–5 (2007).
    Google Scholar 
    Liu, G., Janowitz, G. S. & Kamykowski, D. A biophysical model of population dynamics of the autotrophic dinoflagellate Gymnodinium breve. Mar. Ecol. Prog. Ser. 210, 101–124 (2001).ADS 
    CAS 

    Google Scholar 
    Walsh, J. J. et al. Red tides in the Gulf of Mexico: Where, when, and why?. J. Geophys. Res. 111, C11003 (2006).ADS 

    Google Scholar 
    Bidle, K. D. The molecular ecophysiology of programmed cell death in marine phytoplankton. Ann. Rev. Mar. Sci. 7, 341–375 (2015).PubMed 

    Google Scholar 
    Bidle, K. D. & Bender, S. J. Iron starvation and culture age activate metacaspases and programmed cell death in the marine diatom Thalassiosira pseudonana. Eukaryot. Cell 7, 223–236 (2008).CAS 
    PubMed 

    Google Scholar 
    Bidle, K. D., Haramaty, L., Barcelos, R. J. & Falkowski, P. Viral activation and recruitment of metacaspases in the unicellular coccolithophore, Emiliania huxleyi. Proc. Natl. Acad. Sci. 104, 6049–6054 (2007).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vardi, A. et al. Programmed cell death of the dinoflagellate Peridinium gatunense is mediated by CO2 limitation and oxidative stress. Curr. Biol. 9, 1061–1064 (1999).CAS 
    PubMed 

    Google Scholar 
    Zuppini, A., Andreoli, C. & Baldan, B. Heat stress: An inducer of programmed cell death in Chlorella saccharophila. Plant Cell Physiol. 48, 1000–1009 (2007).CAS 
    PubMed 

    Google Scholar 
    Britt, A. B. DNA damage and repair in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47, 75–100 (1996).CAS 
    PubMed 

    Google Scholar 
    Jimenez, C. et al. Different ways to die: Cell death modes of the unicellular chlorophyte Dunaliella viridis exposed to various environmental stresses are mediated by the caspase-like activity DEVDase. J. Exp. Bot. 60, 815–828 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Moharikar, S., D’Souza, J. S., Kulkarni, A. B. & Rao, B. J. Apoptotic-like cell death pathway is induced in unicellular chlorophyte chlamydomonas reinhardtii (Chlorophyceae) cells following UV irradiation: Detection and functional analyses. J. Phycol. 42, 423–433 (2006).CAS 

    Google Scholar 
    Li, Z., Wakao, S., Fischer, B. B. & Niyogi, K. K. Sensing and responding to excess light. Annu. Rev. Plant Biol. 60, 239–260 (2009).CAS 
    PubMed 

    Google Scholar 
    Niyogi, K. K. Photoprotection revisited: Genetic and molecular approaches. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50, 333–359 (1999).CAS 
    PubMed 

    Google Scholar 
    Apel, K. & Hirt, H. Reactive oxygen species: Metabolism, Oxidative Stress, and Signal Transduction. Annu. Rev. Plant Biol. 55, 373–399 (2004).CAS 
    PubMed 

    Google Scholar 
    Müller, P., Li, X. & Niyogi, K. K. Non-photochemical quenching. A response to excess light energy. Plant Physiol. 125, 1558–1566 (2001).PubMed 
    PubMed Central 

    Google Scholar 
    Bidle, K. D. Programmed cell death in unicellular phytoplankton. Curr. Biol. 26, R594–R607 (2016).CAS 
    PubMed 

    Google Scholar 
    McKay, L., Kamykowski, D., Milligan, E., Schaeffer, B. & Sinclair, G. Comparison of swimming speed and photophysiological responses to different external conditions among three Karenia brevis strains. Harmful Algae 5, 623–636 (2006).CAS 

    Google Scholar 
    Miller-Morey, J. S. & Van Dolah, F. M. Differential responses of stress proteins, antioxidant enzymes, and photosynthetic efficiency to physiological stresses in the Florida red tide dinoflagellate, Karenia brevis. Comp. Biochem. Physiol. Part C Toxicol. Pharmacol. 138, 493–505 (2004).
    Google Scholar 
    Tilney, C. L., Shankar, S., Hubbard, K. A. & Corcoran, A. A. Is Karenia brevis really a low-light-adapted species?. Harmful Algae 90, 101709 (2019).CAS 
    PubMed 

    Google Scholar 
    Yuasa, K., Shikata, T., Kuwahara, Y. & Nishiyama, Y. Adverse effects of strong light and nitrogen deficiency on cell viability, photosynthesis, and motility of the red-tide dinoflagellate Karenia mikimotoi. Phycologia 57, 525–533 (2018).CAS 

    Google Scholar 
    Krause, G. H. & Jahns, P. Non-photochemical energy dissipation determined by chlorophyll fluorescence quenching: Characterization and function. In Chlorophyll a Fluorescence 463–495 (Springer, Netherlands, Cham, 2004).
    Google Scholar 
    Evens, T. J. Photophysiological responses of the toxic red-tide dinoflagellate Gymnodinium breve (Dinophyceae) under natural sunlight. J. Plankton Res. 23, 1177–1194 (2001).CAS 

    Google Scholar 
    Heil, C. A. et al. Influence of daylight surface aggregation behavior on nutrient cycling during a Karenia brevis (Davis) G. Hansen & Ø Moestrup bloom: Migration to the surface as a nutrient acquisition strategy. Harmful Algae 38, 86–94 (2014).CAS 

    Google Scholar 
    Errera, R. Response of the Toxic Dinoflagellate Karenia Brevis to Current and Projected Environmental Conditions. (Texas A&M University, PhD dissertation, 2013).Guillard, R. R. L. & Hargraves, P. E. Stichochrysis immobilis is a diatom, not a chrysophyte. Phycologia 32, 234–236 (1993).
    Google Scholar 
    Dingman, J. E. & Lawrence, J. E. Heat-stress-induced programmed cell death in Heterosigma akashiwo (Raphidophyceae). Harmful Algae 16, 108–116 (2012).
    Google Scholar 
    Lin, Q. et al. Differential cellular responses associated with oxidative stress and cell fate decision under nitrate and phosphate limitations in Thalassiosira pseudonana: Comparative proteomics. PLoS ONE 12(9), e0184849 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Choi, C. J., Brosnahan, M. L., Sehein, T. R., Anderson, D. M. & Erdner, D. L. Insights into the loss factors of phytoplankton blooms: The role of cell mortality in the decline of two inshore Alexandrium blooms. Limnol. Oceanogr. 62, 1742–1753 (2017).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Johnson, J. G., Janech, M. G. & Van Dolah, F. M. Caspase-like activity during aging and cell death in the toxic dinoflagellate Karenia brevis. Harmful Algae 31, 41–53 (2014).CAS 
    PubMed 

    Google Scholar 
    Jauzein, C. & Erdner, D. L. Stress-related responses in Alexandrium tamarense cells exposed to environmental Changes. J. Eukaryot. Microbiol. 60, 526–538 (2013).CAS 
    PubMed 

    Google Scholar 
    Severin, T. & Erdner, D. L. The phytoplankton taxon-dependent oil response and its microbiome: Correlation but not causation. Front. Microbiol. 10, 1–14 (2019).
    Google Scholar 
    Ralph, P. J. & Gademann, R. Rapid light curves: A powerful tool to assess photosynthetic activity. Aquat. Bot. 82, 222–237 (2005).CAS 

    Google Scholar 
    Suzuki, N. & Mittler, R. Reactive oxygen species and temperature stresses: A delicate balance between signaling and destruction. Physiol. Plant. 126, 45–51 (2006).CAS 

    Google Scholar 
    Krause, G. H. & Weis, E. Chlorophyll fluorescence and photosynthesis: The basics. Annu. Rev. Plant Physiol. Plant Mol. Biol. 42, 313–349 (1991).CAS 

    Google Scholar 
    Gechev, T. S. & Hille, J. Hydrogen peroxide as a signal controlling plant programmed cell death. J. Cell Biol. 168, 17–20 (2005).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Miller, G., Suzuki, N., Ciftci-Yilmaz, S. & Mittler, R. Reactive oxygen species homeostasis and signalling during drought and salinity stresses. Plant. Cell Environ. 33, 453–467 (2010).CAS 
    PubMed 

    Google Scholar 
    Purvis, A. C. Role of the alternative oxidase in limiting superoxide production by plant mitochondria. Physiol. Plant. 100, 165–170 (1997).CAS 

    Google Scholar 
    Demmig-Adams, B. & Adams Iii, W. W. Photoprotection and other responses of plants to high light stress. Annu. Rev. Plant Biol. 43, 599–626 (1992).CAS 

    Google Scholar 
    Cui, Y., Zhang, H. & Lin, S. Enhancement of non-photochemical quenching as an adaptive strategy under phosphorus deprivation in the Dinoflagellate Karlodinium veneficum. Front. Microbiol. 8, 1–14 (2017).
    Google Scholar 
    Cassell, R. T., Chen, W., Thomas, S., Liu, L. & Rein, K. S. Brevetoxin, the dinoflagellate neurotoxin, localizes to thylakoid membranes and interacts with the light-harvesting complex II (LHCII) of photosystem II. ChemBioChem 16, 1060–1067 (2015).CAS 
    PubMed 

    Google Scholar 
    Milne, A., Davey, M. S., Worsfold, P. J., Achterberg, E. P. & Taylor, A. R. Real-time detection of reactive oxygen species generation by marine phytoplankton using flow injection-chemiluminescence. Limnol. Oceanogr. Methods 7, 706–715 (2009).CAS 

    Google Scholar 
    Berman-Frank, I. et al. Segregation of nitrogen fixation and oxygenic photosynthesis in the marine cyanobacterium trichodesmium. Science (80-) 294, 1534–1537 (2001).ADS 
    CAS 

    Google Scholar 
    Triantaphylidès, C. et al. Singlet oxygen is the major reactive oxygen species involved in photooxidative damage to plants. Plant Physiol. 148, 960–968 (2008).PubMed 
    PubMed Central 

    Google Scholar 
    Gao, Y. & Erdner, D. L. Dynamics of cell death across growth stages and the diel cycle in the dinoflagellate Karenia brevis. J. Eukaryot. Microbiol. https://doi.org/10.1111/jeu.12874 (2021).Article 
    PubMed 

    Google Scholar 
    Xu, K., Jiang, H., Juneau, P. & Qiu, B. Comparative studies on the photosynthetic responses of three freshwater phytoplankton species to temperature and light regimes. J. Appl. Phycol. 24, 1113–1122 (2012).CAS 

    Google Scholar 
    Yamori, W., Makino, A. & Shikanai, T. A physiological role of cyclic electron transport around photosystem I in sustaining photosynthesis under fluctuating light in rice. Sci. Rep. 6, 20147 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Berman-Frank, I., Bidle, K. D., Haramaty, L. & Falkowski, P. G. The demise of the marine cyanobacterium, Trichodesmium spp., via an autocatalyzed cell death pathway. Limnol. Oceanogr. 49, 997–1005 (2004).ADS 

    Google Scholar  More

  • in

    Adaptive phenotypic plasticity is under stabilizing selection in Daphnia

    Scheiner, S. M. Genetics and evolution of phenotypic plasticity. Annu. Rev. Ecol. Syst. 24, 35–68 (1993).Article 

    Google Scholar 
    Via, S. et al. Adaptive phenotypic plasticity: consensus and controversy. Trends Ecol. Evol. 10, 212–217 (1995).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ghalambor, C. K. et al. Adaptive versus non‐adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments. Funct. Ecol. 21, 394–407 (2007).Article 

    Google Scholar 
    King, J. G. & Hadfield, J. D. The evolution of phenotypic plasticity when environments fluctuate in time and space. Evol. Lett. 3, 15–27 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Newman, R. A. Genetic variation for phenotypic plasticity in the larval life history of spadefoot toads (Scaphiopus couchii). Evolution 48, 1773–1785 (1994).PubMed 

    Google Scholar 
    Nussey, D. H. et al. Selection on heritable phenotypic plasticity in a wild bird population. Science 310, 304–306 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    Scheiner, S. Selection experiments and the study of phenotypic plasticity 1. J. Evol. Biol. 15, 889–898 (2002).Article 

    Google Scholar 
    Ghalambor, C. K. et al. Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature. Nature 525, 372–375 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Reger, J. et al. Predation drives local adaptation of phenotypic plasticity. Nat. Ecol. Evol. 2, 100–107 (2018).PubMed 
    Article 

    Google Scholar 
    Sommer, R. J. Phenotypic plasticity: from theory and genetics to current and future challenges. Genetics 215, 1–13 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Brakefield, P. M. & Reitsma, N. Phenotypic plasticity, seasonal climate and the population biology of Bicyclus butterflies (Satyridae) in Malawi. Ecol. Entomol. 16, 291–303 (1991).Article 

    Google Scholar 
    Rountree, D. & Nijhout, H. Hormonal control of a seasonal polyphenism in Precis coenia (Lepidoptera: Nymphalidae). J. Insect Physiol. 41, 987–992 (1995).CAS 
    Article 

    Google Scholar 
    Scheiner, S. M. & Holt, R. D. The genetics of phenotypic plasticity. X. Variation versus uncertainty. Ecol. Evol. 2, 751–767 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bonamour, S. et al. Phenotypic plasticity in response to climate change: the importance of cue variation. Philos. Trans. R. Soc. B 374, 20180178 (2019).Article 

    Google Scholar 
    Fox, R.J., Donelson, J. M., Schunter, C., Ravasi, T. & Gaitán-Espitia, J. D. Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change. Philos. Trans. R. Soc. B https://doi.org/10.1098/rstb.2018.0174 (2019).Auld, J. R., Agrawal, A. A. & Relyea, R. A. Re-evaluating the costs and limits of adaptive phenotypic plasticity. Proc. R. Soc. B 277, 503–511 (2010).PubMed 
    Article 

    Google Scholar 
    Murren, C. J. et al. Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity. Heredity 115, 293–301 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Yampolsky, L. Y., Schaer, T. M. & Ebert, D. Adaptive phenotypic plasticity and local adaptation for temperature tolerance in freshwater zooplankton. Proc. R. Soc. B 281, 20132744 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schmid, M. & Guillaume, F. The role of phenotypic plasticity on population differentiation. Heredity 119, 214–225 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Charlesworth, B., Lande, R. & Slatkin, M. A neo-Darwinian commentary on macroevolution. Evolution 36, 474–498 (1982).PubMed 

    Google Scholar 
    Lynch, M. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. Am. Nat. 136, 727–741 (1990).Article 

    Google Scholar 
    Kingsolver, J. G. & Pfennig, D. W. Patterns and power of phenotypic selection in nature. Bioscience 57, 561–572 (2007).Article 

    Google Scholar 
    West-Eberhard, M. J. Developmental plasticity and the origin of species differences. Proc. Natl Acad. Sci. USA 102, 6543–6549 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Turelli, M. & Barton, N. Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and G × E interactions. Genetics 166, 1053–1079 (2004).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Charlesworth, B. Causes of natural variation in fitness: evidence from studies of Drosophila populations. Proc. Natl Acad. Sci. USA 112, 1662–1669 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Noble, D. W., Radersma, R. & Uller, T. Plastic responses to novel environments are biased towards phenotype dimensions with high additive genetic variation. Proc. Natl Acad. Sci. USA 116, 13452–13461 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Draghi, J. A. & Whitlock, M. C. Phenotypic plasticity facilitates mutational variance, genetic variance, and evolvability along the major axis of environmental variation. Evolution 66-9, 2891–2902 (2012).Article 

    Google Scholar 
    Houle, D. How should we explain variation in the genetic variance of traits? Genetica 102, 241–253 (1998).PubMed 
    Article 

    Google Scholar 
    Tollrian, R. Predator‐induced morphological defenses: costs, life history shifts, and maternal effects in Daphnia pulex. Ecology 76, 1691–1705 (1995).Article 

    Google Scholar 
    Agrawal, A. A., Laforsch, C. & Tollrian, R. Transgenerational induction of defences in animals and plants. Nature 401, 60–63 (1999).CAS 
    Article 

    Google Scholar 
    Tollrian, R. Neckteeth formation in Daphnia pulex as an example of continuous phenotypic plasticity: morphological effects of Chaoborus kairomone concentration and their quantification. J. Plankton Res. 15, 1309–1318 (1993).Article 

    Google Scholar 
    Dennis, S. et al. Phenotypic convergence along a gradient of predation risk. Proc. R. Soc. B 278, 1687–1696 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hammill, E. & Beckerman, A. P. Reciprocity in predator–prey interactions: exposure to defended prey and predation risk affects intermediate predator life history and morphology. Oecologia 163, 193–202 (2010).PubMed 
    Article 

    Google Scholar 
    Hammill, E., Rogers, A. & Beckerman, A. P. Costs, benefits and the evolution of inducible defences: a case study with Daphnia pulex. J. Evol. Biol. 21, 705–715 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Barnard-Kubow, K. et al. Polygenic variation in sexual investment across an ephemerality gradient in Daphnia pulex. Mol. Bio. Evol. 39, msac121 (2022).Article 

    Google Scholar 
    Deng, H.-W. & Lynch, M. Inbreeding depression and inferred deleterious-mutation parameters in Daphnia. Genetics 147, 147–155 (1997).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Seyfert, A. L. et al. The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics 178, 2113–2121 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Xu, S. et al. High mutation rates in the mitochondrial genomes of Daphnia pulex. Mol. Biol. Evol. 29, 763–769 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Collyer, M. L. & Adams, D. C. Phenotypic trajectory analysis: comparison of shape change patterns in evolution and ecology. Hystrix 24, 75 (2013).
    Google Scholar 
    Adams, D.C., Collyer, M., Kaliontzopoulou, A. & Sherratt, E. et al. Geomorph: software for geometric morphometric analyses (University of New England, 2016); https://hdl.handle.net/1959.11/21330Adams, D. C. & Collyer, M. L. Comparing the strength of modular signal, and evaluating alternative modular hypotheses, using covariance ratio effect sizes with morphometric data. Evolution 73, 2352–2367 (2019).PubMed 
    Article 

    Google Scholar 
    Richards, C. L., Bossdorf, O. & Pigliucci, M. What role does heritable epigenetic variation play in phenotypic evolution? BioScience 60, 232–237 (2010).Article 

    Google Scholar 
    Latta, L. C. IV et al. The phenotypic effects of spontaneous mutations in different environments. Am. Nat. 185, 243–252 (2015).PubMed 
    Article 

    Google Scholar 
    Lind, M. I. et al. The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection. Proc. R. Soc. B 282, 20151651 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Laforsch, C. & Tollrian, R. Inducible defenses in multipredator environments: cyclomorphosis in Daphnia cucullata. Ecology 85, 2302–2311 (2004).Article 

    Google Scholar 
    Weiss, L. C., Leimann, J. & Tollrian, R. Predator-induced defences in Daphnia longicephala: location of kairomone receptors and timeline of sensitive phases to trait formation. J. Exp. Biol. 218, 2918–2926 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Tollrian, R. & Harvell, C.D. The Ecology and Evolution of Inducible Defenses (Princeton Univ. Press, 1999).Lande, R. Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation. J. Evol. Biol. 22, 1435–1446 (2009).PubMed 
    Article 
    CAS 

    Google Scholar 
    Via, S. & Lande, R. Genotype–environment interaction and the evolution of phenotypic plasticity. Evolution 39, 505–522 (1985).PubMed 
    Article 

    Google Scholar 
    Kvist, J. et al. Temperature treatments during larval development reveal extensive heritable and plastic variation in gene expression and life history traits. Mol. Ecol. 22, 602–619 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Siepielski, A. M. et al. Differences in the temporal dynamics of phenotypic selection among fitness components in the wild. Proc. R. Soc. B 278, 1572–1580 (2011).PubMed 
    Article 

    Google Scholar 
    Muschick, M. et al. Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation. BMC Evol. Biol. 11, 116 (2011).Salzburger, W. Understanding explosive diversification through cichlid fish genomics. Nat. Rev. Genet. 19, 705–717 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Halligan, D. L. & Keightley, P. D. Spontaneous mutation accumulation studies in evolutionary genetics. Annu. Rev. Ecol. Evol. Syst. 40, 151–172 (2009).Article 

    Google Scholar 
    Houle, D., Morikawa, B. & Lynch, M. Comparing mutational variabilities. Genetics 143, 1467–1483 (1996).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Eberle, S. et al. Hierarchical assessment of mutation properties in Daphnia magna. G3 Genes Genomes Genetics 8, 3481–3487 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Stenseth, N. C. et al. Ecological effects of climate fluctuations. Science 297, 1292–1296 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    Burgmer, T., Hillebrand, H. & Pfenninger, M. Effects of climate-driven temperature changes on the diversity of freshwater macroinvertebrates. Oecologia 151, 93–103 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Yan, N. D. et al. Long-term trends in zooplankton of Dorset, Ontario, lakes: the probable interactive effects of changes in pH, total phosphorus, dissolved organic carbon, and predators. Can. J. Fish. Aquat. Sci. 65, 862–877 (2008).CAS 
    Article 

    Google Scholar 
    Reed, T. E., Schindler, D. E. & Waples, R. S. Interacting effects of phenotypic plasticity and evolution on population persistence in a changing climate. Conserv. Biol. 25, 56–63 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    ASTM, Standard Guide for Conducting Acute Toxicity Tests with Fishes, Macroinvertebrates, and Amphibians (American Society for Testing and Materials, 1988).Baym, M. et al. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS ONE 10, e0128036 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang, J. et al. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).MarkDuplicates v.2.20 (Broad Institute, 2019); http://broadinstitute.github.io/picardMcKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Poplin, R. et al. Scaling accurate genetic variant discovery to tens of thousands of samples. Preprint at bioRxiv https://doi.org/10.1101/201178 (2018).Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326–3328 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Manichaikul, A. et al. Robust relationship inference in genome-wide association studies. Bioinformatics 26, 2867–2873 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Beckerman, A. P., Rodgers, G. M. & Dennis, S. R. The reaction norm of size and age at maturity under multiple predator risk. J. Anim. Ecol. 79, 1069–1076 (2010).PubMed 
    Article 

    Google Scholar 
    Naraki, Y., Hiruta, C. & Tochinai, S. Identification of the precise kairomone-sensitive period and histological characterization of necktooth formation in predator-induced polyphenism in Daphnia pulex. Zool. Sci. 30, 619–625 (2013).Article 

    Google Scholar 
    Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Scrucca, L. et al. mclust 5: clustering, classification and density estimation using Gaussian finite mixture models. R J. 8, 289 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Fox, J. & Weisberg, S. An R Companion to Applied Regression (Sage, 2018).Ben-Shachar, M. S., Lüdecke, D. & Makowski, D. effectsize: estimation of effect size indices and standardized parameters. J. Open Source Softw. 5, 2815 (2020).Article 

    Google Scholar 
    Collyer, M. L. & Adams, D. C. RRPP: an r package for fitting linear models to high‐dimensional data using residual randomization. Methods Ecol. Evol. 9, 1772–1779 (2018).Article 

    Google Scholar 
    Collyer, M., Adams, D. & and Collyer, M.M. RRPP: linear model evaluation with randomized residuals in a permutation procedure. R package version 1.3 https://CRAN.R-project.org/package=RRPP (2021).Smirnov, P. robcor: Robust correlations. R package version 0.1-6.1 https://CRAN.R-project.org/package=ropcor (2014).Hadfield, J. D. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J. Stat. Softw. 33, 1–22 (2010).Article 

    Google Scholar 
    Yang, J. et al. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76–82 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2017).Villanueva, R., Chen, Z. & Wickham, H. ggplot2: Elegant Graphics for Data Analysis Using the Grammar of Graphics (Springer-Verlag, 2016).Wilke, C. cowplot: Streamlined plot theme and plot annotations for ‘ggplot2’. R package version 0.9. 2 https://CRAN.R-project.org/package=cowplot (2020).Dowle, M. et al. data.table: Extension of ‘data.frame‘. R package version 1.14.0 https://CRAN.R-project.org/package=data.table (2021).Daniel, M. foreach: Provides foreach looping construct. R package version 1.5.1 https://CRAN.R-project.org/package=foreach (2020).Weston, S. doMC: Foreach parallel adaptor for ‘parallel’. R package version 1.3.7 https://CRAN.R-project.org/package=doMC (2020).Clarke, E. & Sherrill-Mix, S. Ggbeeswarm: Categorical scatter (violin point) plots. R package version 0.6. 0 https://CRAN.R-project.org (2017).Garnier, S. et al. viridis: Default color maps from ‘matplotlib’. R package version 0.5.1 (2018). More

  • in

    A network simplification approach to ease topological studies about the food-web architecture

    Ecological networks: Linking structure to dynamics in food webs. (Oxford University Press, 2006).Adaptive food webs: Stability and transitions of real and model ecosystems. (Cambridge University Press, 2018).Pimm, S. L. Food Webs (Springer, 1982).Book 

    Google Scholar 
    Adaptive Food Webs: Stability and Transitions of Real and Model Ecosystems. (Cambridge University Press, 2017). doi:https://doi.org/10.1017/9781316871867.da Mata, A. S. Complex Networks: A Mini-review. Braz. J. Phys. 50, 658–672 (2020).ADS 
    Article 

    Google Scholar 
    Zhang, W. Fundamentals of Network Biology. (World Scientific (Europe), 2018). https://doi.org/10.1142/q0149.Reichman, O. J., Jones, M. B. & Schildhauer, M. P. Challenges and opportunities of open data in ecology. Science 331, 703–705 (2011).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Farley, S. S., Dawson, A., Goring, S. J. & Williams, J. W. situating ecology as a big-data science: Current advances, challenges, and solutions. Bioscience 68, 563–576 (2018).Article 

    Google Scholar 
    Osawa, T. Perspectives on biodiversity informatics for ecology. Ecol. Res. 34, 446–456 (2019).Article 

    Google Scholar 
    Shin, N. et al. Toward more data publication of long-term ecological observations. Ecol. Res. 35, 700–707 (2020).Article 

    Google Scholar 
    Pringle, R. M. & Hutchinson, M. C. Resolving food-web structure. Annu. Rev. Ecol. Evol. Syst. 51, 55–80 (2020).Article 

    Google Scholar 
    Derocles, S. A. P. et al. Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis. in Advances in Ecological Research vol. 58 1–62 (Elsevier, 2018).Vacher, C. et al. Learning ecological networks from next-generation sequencing data. in Advances in Ecological Research vol. 54, 1–39 (Elsevier, 2016).Evans, D. M., Kitson, J. J. N., Lunt, D. H., Straw, N. A. & Pocock, M. J. O. Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems. Funct. Ecol. 30, 1904–1916 (2016).Article 

    Google Scholar 
    Pocock, M. J. O. et al. A vision for global biodiversity monitoring with citizen science. in Advances in Ecological Research vol. 59, 169–223 (Elsevier, 2018).Sultana, M. & Storch, I. Suitability of open digital species records for assessing biodiversity patterns in cities: A case study using avian records. J. Urban Ecol. 7, juab014 (2021).Article 

    Google Scholar 
    Amano, T., Lamming, J. D. L. & Sutherland, W. J. Spatial gaps in global biodiversity information and the role of citizen science. Bioscience 66, 393–400 (2016).Article 

    Google Scholar 
    Chandler, M. et al. Contribution of citizen science towards international biodiversity monitoring. Biol. Conserv. 213, 280–294 (2017).Article 

    Google Scholar 
    Fontaine, C. et al. The ecological and evolutionary implications of merging different types of networks: Merging networks with different interaction types. Ecol. Lett. 14, 1170–1181 (2011).PubMed 
    Article 

    Google Scholar 
    Martinson, H. M. & Fagan, W. F. Trophic disruption: A meta-analysis of how habitat fragmentation affects resource consumption in terrestrial arthropod systems. Ecol. Lett. 17, 1178–1189 (2014).PubMed 
    Article 

    Google Scholar 
    Marczak, L. B., Thompson, R. M. & Richardson, J. S. Meta-analysis: Trophic level, Habitat, and productivity shape the food web effects of resource subsidies. Ecology 88, 140–148 (2007).PubMed 
    Article 

    Google Scholar 
    McCary, M. A., Mores, R., Farfan, M. A. & Wise, D. H. Invasive plants have different effects on trophic structure of green and brown food webs in terrestrial ecosystems: A meta-analysis. Ecol. Lett. 19, 328–335 (2016).PubMed 
    Article 

    Google Scholar 
    Cirtwill, A. R., Stouffer, D. B. & Romanuk, T. N. Latitudinal gradients in biotic niche breadth vary across ecosystem types. Proc. R. Soc. B Biol. Sci. 282, 20151589 (2015).Article 
    CAS 

    Google Scholar 
    Fortuna, M. A., Ortega, R. & Bascompte, J. The Web of Life. ArXiv14032575 Q-Bio (2014).Brose, U. et al. Predator traits determine food-web architecture across ecosystems. Nat. Ecol. Evol. 3, 919–927 (2019).PubMed 
    Article 

    Google Scholar 
    Mace, G. M., Norris, K. & Fitter, A. H. Biodiversity and ecosystem services: A multilayered relationship. Trends Ecol. Evol. 27, 19–26 (2012).PubMed 
    Article 

    Google Scholar 
    Keyes, A. A., McLaughlin, J. P., Barner, A. K. & Dee, L. E. An ecological network approach to predict ecosystem service vulnerability to species losses. Nat. Commun. 12, 1586 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Peng, J. et al. Linking ecosystem services and circuit theory to identify ecological security patterns. Sci. Total Environ. 644, 781–790 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Su, Y. et al. Modeling the optimal ecological security pattern for guiding the urban constructed land expansions. Urban For. Urban Green. 19, 35–46 (2016).Article 

    Google Scholar 
    Kowarik, I. Novel urban ecosystems, biodiversity, and conservation. Environ. Pollut. 159, 1974–1983 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Di Marco, M., Watson, J. E. M., Venter, O. & Possingham, H. P. Global biodiversity targets require both sufficiency and efficiency. Conserv. Lett. 9, 395–397 (2016).Article 

    Google Scholar 
    Kim, K.-H. & Pauleit, S. Landscape character, biodiversity and land use planning: The case of Kwangju City Region, South Korea. Land Use Policy 24, 264–274 (2007).Article 

    Google Scholar 
    Young, J. et al. Towards sustainable land use: Identifying and managing the conflicts between human activities and biodiversity conservation in Europe. Biodivers. Conserv. 14, 1641–1661 (2005).Article 

    Google Scholar 
    Dardonville, M., Urruty, N., Bockstaller, C. & Therond, O. Influence of diversity and intensification level on vulnerability, resilience and robustness of agricultural systems. Agric. Syst. 184, 102913 (2020).Article 

    Google Scholar 
    Oliver, T. H. et al. Biodiversity and resilience of ecosystem functions. Trends Ecol. Evol. 30, 673–684 (2015).PubMed 
    Article 

    Google Scholar 
    Lau, M. K., Borrett, S. R., Baiser, B., Gotelli, N. J. & Ellison, A. M. Ecological network metrics: Opportunities for synthesis. Ecosphere 8, e01900 (2017).Article 

    Google Scholar 
    Newman, M. E. J. Networks. (Oxford University Press, 2018).Levine, S. Several measures of trophic structure applicable to complex food webs. J. Theor. Biol. 83, 195–207 (1980).ADS 
    Article 

    Google Scholar 
    Guimarães, P. R. The structure of ecological networks across levels of organization. Annu. Rev. Ecol. Evol. Syst. 51, 433–460 (2020).Article 

    Google Scholar 
    Dormann, C. F., Frund, J., Bluthgen, N. & Gruber, B. Indices, graphs and null models: Analyzing bipartite ecological networks. Open Ecol. J. 2, 7–24 (2009).Article 

    Google Scholar 
    Jordán, F., Benedek, Z. & Podani, J. Quantifying positional importance in food webs: A comparison of centrality indices. Ecol. Model. 205, 270–275 (2007).Article 

    Google Scholar 
    Jordán, F., Liu, W. & Davis, A. J. Topological keystone species: Measures of positional importance in food webs. Oikos 112, 535–546 (2006).Article 

    Google Scholar 
    Jordán, F., Okey, T. A., Bauer, B. & Libralato, S. Identifying important species: Linking structure and function in ecological networks. Ecol. Model. 216, 75–80 (2008).Article 

    Google Scholar 
    Jiang, L. Determination of keystone species in CSM food web: A topological analysis of network structure. Netw. Biol. 5, 13 (2015).
    Google Scholar 
    Abarca-Arenas, L. G., Franco-Lopez, J., Peterson, M. S., Brown-Peterson, N. J. & Valero-Pacheco, E. Sociometric analysis of the role of penaeids in the continental shelf food web off Veracruz. Mexico Based By-catch Fish. Res. 87, 46–57 (2007).
    Google Scholar 
    Abascal-Monroy, I. M. et al. Functional and structural food web comparison of Terminos Lagoon, Mexico in Three Periods (1980, 1998, and 2011). Estuaries Coasts 39, 1282–1293 (2016).Article 

    Google Scholar 
    McDonald-Madden, E. et al. Using food-web theory to conserve ecosystems. Nat. Commun. 7, 10245 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Windsor, F. M. et al. Identifying plant mixes for multiple ecosystem service provision in agricultural systems using ecological networks. J. Appl. Ecol. 58, 2770–2782 (2021).Article 

    Google Scholar 
    Klaise, J. & Johnson, S. The origin of motif families in food webs. Sci. Rep. 7, 16197 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Estrada, E. Characterization of topological keystone species. Ecol. Complex. 4, 48–57 (2007).Article 

    Google Scholar 
    Thompson, R. M. & Townsend, C. R. Impacts on stream food webs of native and exotic forest: An intercontinental comparison. Ecology 84, 145–161 (2003).Article 

    Google Scholar 
    Bascompte, J., Melian, C. J. & Sala, E. Interaction strength combinations and the overfishing of a marine food web. Proc. Natl. Acad. Sci. 102, 5443–5447 (2005).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Dunne, J. A. et al. The roles and impacts of human hunter-gatherers in North Pacific marine food webs. Sci. Rep. 6, 21179 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gauzens, B., Legendre, S., Lazzaro, X. & Lacroix, G. Food-web aggregation, methodological and functional issues. Oikos 122, 1606–1615 (2013).Article 

    Google Scholar 
    Patonai, K. & Jordán, F. Aggregation of incomplete food web data may help to suggest sampling strategies. Ecol. Model. 352, 77–89 (2017).Article 

    Google Scholar 
    Thompson, R. M. & Townsend, C. R. Is resolution the solution?: The effect of taxonomic resolution on the calculated properties of three stream food webs. Freshw. Biol. 44, 413–422 (2000).Article 

    Google Scholar 
    Abarca-Arenas, L. G. & Ulanowicz, R. E. The effects of taxonomic aggregation on network analysis. Ecol. Model. 149, 285–296 (2002).Article 

    Google Scholar 
    Jordán, F. & Osváth, G. The sensitivity of food web topology to temporal data aggregation. Ecol. Model. 220, 3141–3146 (2009).Article 

    Google Scholar 
    European Commission. Communication from the commission to the european parliament, the council, the european economic and social committee and the committee of the regions: EU Biodiversity Strategy for 2030 Bringing nature back into our lives. Preprint at https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:52020DC0380 (2020).European Parliament. European Parliament resolution of 9 June 2021 on the EU Biodiversity Strategy for 2030: Bringing nature back into our lives (P9_TA(2021)0277). Preprint at https://www.europarl.europa.eu/doceo/document/TA-9-2021-0277_EN.html (2021).Felson, A. J. & Ellison, A. M. Designing (for) Urban Food Webs. Front. Ecol. Evol. 9, 582041 (2021).Article 

    Google Scholar 
    Warren, P. et al. Urban food webs: Predators, prey, and the people who feed them. Bull. Ecol. Soc. Am. 87, 387–393 (2006).Article 

    Google Scholar 
    De Montis, A., Ganciu, A., Cabras, M., Bardi, A. & Mulas, M. Comparative ecological network analysis: An application to Italy. Land Use Policy 81, 714–724 (2019).Article 

    Google Scholar 
    Poisot, T. et al. Mangal—making ecological network analysis simple. Ecography 39, 384–390 (2016).Article 

    Google Scholar 
    Morris, Z. B., Weissburg, M. & Bras, B. Ecological network analysis of urban–industrial ecosystems. J. Ind. Ecol. 25, 193–204 (2021).Article 

    Google Scholar 
    Chamberlain, S. A. & Szöcs, E. taxize: Taxonomic search and retrieval in R. F1000 Research 2, 191 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hagberg, A. A., Schult, D. A. & Swart, P. J. Exploring network structure, dynamics, and function using networkX. in Proceedings of the 7th Python in Science Conference (eds. Varoquaux, G., Vaught, T. & Millman, J.) 11–15 (2008).Scotti, M. & Jordán, F. Relationships between centrality indices and trophic levels in food webs. Community Ecol. 11, 59–67 (2010).Article 

    Google Scholar 
    Gouveia, C., Móréh, Á. & Jordán, F. Combining centrality indices: Maximizing the predictability of keystone species in food webs. Ecol. Indic. 126, 107617 (2021).Article 

    Google Scholar 
    Allesina, S. & Pascual, M. Googling Food Webs: Can an Eigenvector Measure Species’ Importance for Coextinctions?. PLoS Comput. Biol. 5, e1000494 (2009).ADS 
    MathSciNet 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Patro, S. G. K. & Sahu, K. K. Normalization: A preprocessing stage. https://doi.org/10.48550/ARXIV.1503.06462(2015).Reback, J. et al. pandas-dev/pandas: Pandas 1.2.3. (Zenodo, 2021). 10.5281/ZENODO.4572994.Hunter, J. D. Matplotlib: A 2D graphics environment. Comput. Sci. Eng. 9, 90–95 (2007).Article 

    Google Scholar 
    Waskom, M. et al. mwaskom/seaborn: v0.11.1 (December 2020). (Zenodo, 2020). 10.5281/ZENODO.4379347.Girvan, M. & Newman, M. E. J. Community structure in social and biological networks. Proc. Natl. Acad. Sci. 99, 7821–7826 (2002).ADS 
    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 
    MATH 
    Article 

    Google Scholar 
    Rosvall, M., Axelsson, D. & Bergstrom, C. T. The map equation. Eur. Phys. J. Spec. Top. 178, 13–23 (2009).Article 

    Google Scholar 
    Gao, P. & Kupfer, J. A. Uncovering food web structure using a novel trophic similarity measure. Ecol. Inform. 30, 110–118 (2015).Article 

    Google Scholar 
    Gauzens, B., Thébault, E., Lacroix, G. & Legendre, S. Trophic groups and modules: Two levels of group detection in food webs. J. R. Soc. Interface 12, 20141176 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rudiger, P. et al. holoviz/holoviews: Version 1.14.2. (Zenodo, 2021). 10.5281/ZENODO.4581995.Pedregosa, F. et al. Scikit-learn: Machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).MathSciNet 
    MATH 

    Google Scholar  More

  • in

    The origin and evolution of open habitats in North America inferred by Bayesian deep learning models

    DataSpatial and temporal rangeWe focused on a geographic area that is defined by a cropping window with the corner points P1 (Lon = −180, Lat = 25) and P2 (Lon = −52, Lat = 80), covering the majority of the North American continent (e.g., Fig. 3). We focused on the last 30 Myr, a time span encompassing most of our available sites with paleovegetation information (Supplementary Fig. 1). From the following data sources, we only selected those data points that fall within this spatiotemporal range.Our approach described below required discretizing the input data of past vegetation labels and fossil occurrences into time-bins. For this, we chose the age boundaries of geological stages defined in the International Chronostratigraphic Chart, v2020/0345, since these stages are expected to represent meaningful temporal units for analyzing both faunal and floral patterns. A total of 17 geological stages fell within our selected time frame of the last 30 Myr. We discretized the ages of all data points (vegetation data and fossil occurrences) that fell within a given stage by setting them to the midpoint of the respective stage.Paleovegetation dataWe reviewed a large body of peer-reviewed literature containing paleovegetation reconstructions and compiled a database of 331 sites with paleovegetation data for North America (Supplementary Data 1). These sites represent individual vegetation reconstructions based on fossil evidence (phytoliths, pollen, macrofossil assemblages) of distinct locations in time and space. We condensed the vegetation interpretation of the compiled vegetation data, which in many cases described specific vegetation ecosystem components, into the broader labels “open” versus “closed” vegetation. This resulted in 180 sites being labeled as closed and 151 as open, their dating rounded to the midpoint of the nearest geological stage (Supplementary Data 1). For several of these sites we found multiple vegetation reconstructions in the reviewed literature, for example when multiple sediment samples were taken from the same horizon of a given formation, belonging to the same geological stage. We treated these spatiotemporal duplicates as a single data point, excluding sites with mixed vegetation information (i.e., containing both open and closed vegetation reconstructions).Current vegetation dataTo supplement the limited number of paleovegetation sites, we compiled data about the current vegetation within our study area. In order to obtain current vegetation patterns, we downloaded the SYNMAP Global Potential Vegetation data29. As for the paleovegetation data, we collapsed the more detailed biome data into broader categories by coding the SYNMAP biome IDs  More