Ecology

1.
Sardain, A., Sardain, E. & Leung, B. Global forecasts of shipping traffic and biological invasions to 2050. Nat. Sustain. 2, 274–282 (2019).
Article  Google Scholar 
2.
Pecl, G. T. et al. Biodiversity redistribution under climate change: impacts on ecosystems and human well-being. Science 355, eaai9214 (2017).
PubMed  Article  CAS  Google Scholar 

3.
Pöysä, H. et al. Changes in species richness and composition of boreal waterbird communities: a comparison between two time periods 25 years apart. Sci. Rep. 9, 1725 (2019).
PubMed  PubMed Central  Article  CAS  Google Scholar 

4.
Underwood, G. J. C. et al. Organic matter from Arctic sea-ice loss alters bacterial community structure and function. Nat. Clim. Change 9, 170–176 (2019).
Article  Google Scholar 

5.
Kubicek, A., Breckling, B., Hoegh-Guldberg, O. & Reuter, H. Climate change drives trait-shifts in coral reef communities. Sci. Rep. 9, 3721 (2019).
PubMed  PubMed Central  Article  CAS  Google Scholar 

6.
Poloczanska, E. S. et al. Global imprint of climate change on marine life. Nat. Clim. Change 3, 919–925 (2013).
Article  Google Scholar 

7.
Hastings, A. Timescales, dynamics, and ecological understanding. Ecology 91, 3471–3480 (2010).
PubMed  Article  Google Scholar 

8.
Hastings, A. Timescales and the management of ecological systems. Proc. Natl Acad. Sci. USA 113, 14568–14573 (2016).
CAS  PubMed  Article  Google Scholar 

9.
Hastings, A. Transients: the key to long-term ecological understanding? Trends Ecol. Evol. 19, 39–45 (2004).
PubMed  Article  Google Scholar 

10.
Hastings, A. & Higgins, K. Persistence of transients in spatially structured ecological models. Science 263, 1133–1136 (1994).
CAS  PubMed  Article  Google Scholar 

11.
Hastings, A. Transient dynamics and persistence of ecological systems. Ecol. Lett. 4, 215–220 (2001).
Article  Google Scholar 

12.
Likens, G. E. (ed.) Long-Term Studies in Ecology: Approaches and Alternatives (Springer, 1989).

13.
Franklin, J. F., Bledsoe, C. S. & Callahan, J. T. Contributions of the Long-term Ecological Research program. Bioscience 40, 509–523 (1990).
Article  Google Scholar 

14.
Ratajczak, Z. et al. The interactive effects of press/pulse intensity and duration on regime shifts at multiple scales. Ecol. Monogr. 87, 198–218 (2017).
Article  Google Scholar 

15.
Hastings, A. et al. Transient phenomena in ecology. Science 361, eaat6412 (2018).
PubMed  Article  CAS  Google Scholar 

16.
Morozov, A. et al. Long transients in ecology: theory and applications. Phys. Life Rev. 32, 1–40 (2020).
PubMed  Article  Google Scholar 

17.
Holling, C. S. Adaptive Environmental Assessment and Management (International Institute for Applied Systems Analysis, 1978).

18.
Walters, C. Adaptive Management of Renewable Resources (Macmillan, 1986).

19.
Lee, K. N. Appraising adaptive management. Conserv. Ecol. 3, 3 (1999).
Article  Google Scholar 

20.
Gunderson, L. & Light, S. S. Adaptive management and adaptive governance in the Everglades ecosystem. Policy Sci. 39, 323–334 (2006).
Article  Google Scholar 

21.
Franklin, J. Biological legacies: a critical management concept from Mount St. Helens. In Trans. 55th North American Wildlife and Natural Resources Conference (1990).

22.
Funk, J. L. et al. Keys to enhancing the value of invasion ecology research for management. Biol. Invasions https://doi.org/10.1007/s10530-020-02267-9 (2020).

23.
Beaury, E. M. et al. Incorporating climate change into invasive species management: insights from managers. Biol. Invasions 22, 233–252 (2020).
Article  Google Scholar 

24.
Cuddington, K. et al. Process-based models are required to manage ecological systems in a changing world. Ecosphere https://doi.org/10.1890/ES12-00178.1 (2013).

25.
White, J. W., Botsford, L. W., Hastings, A., Baskett, M. L. & Kaplan, D. M. Transient responses of fished populations to marine reserve establishment. Conserv. Lett. 6, 180–191 (2013).
Article  Google Scholar 

26.
Kaplan, K. A. et al. Setting expected timelines of fished population recovery for the adaptive management of a marine protected area network. Ecol. Appl. https://doi.org/10.1002/eap.1949 (2019).

27.
Hopf, J. K., Jones, G. P., Williamson, D. H. & Connolly, S. R. Marine reserves stabilize fish populations and fisheries yields in disturbed coral reef systems. Ecol. Appl. 29, e01905 (2019).
PubMed  Article  Google Scholar 

28.
Caselle, J. E., Davis, K. & Marks, L. M. Marine management affects the invasion success of a non-native species in a temperate reef system in California, USA. Ecol. Lett. 21, 43–53 (2018).
PubMed  Article  Google Scholar 

29.
Mahmood, A. H. et al. Comparison of techniques to control the aggressive environmental invasive species Galenia pubescens in a degraded grassland reserve, Victoria, Australia. PLoS ONE 13, 1–16 (2018).
Google Scholar 

30.
Liebhold, A. M. et al. Eradication of invading insect populations: from concepts to applications. Annu. Rev. Entemol. 61, 335–352 (2016).
CAS  Article  Google Scholar 

31.
Isbell, F. et al. Nutrient enrichment, biodiversity loss, and consequent declines in ecosystem productivity. Proc. Natl Acad. Sci. USA 110, 11911–11916 (2013).
CAS  PubMed  Article  PubMed Central  Google Scholar 

32.
Clark, C. M. & Tilman, D. Recovery of plant diversity following N cessation: effects of recruitment, litter, and elevated N cycling. Ecology 91, 3620–3630 (2010).
PubMed  Article  PubMed Central  Google Scholar 

33.
Storkey, J. et al. Grassland biodiversity bounces back from long-term nitrogen addition. Nature 528, 401–404 (2015).
CAS  PubMed  Article  PubMed Central  Google Scholar 

34.
Brettin, A. Ecological Management Practices Informed by Flow–Kick Dynamics. PhD thesis, Univ. Minnesota (2019).

35.
Meyer, K. et al. Quantifying resilience to recurrent ecosystem disturbances using flow–kick dynamics. Nat. Sustain. 1, 671–678 (2018).
Article  Google Scholar 

36.
Schindler, D. W. The dilemma of controlling cultural eutrophication of lakes. Proc. R. Soc. B 279, 4322–4333 (2012).
CAS  PubMed  Article  PubMed Central  Google Scholar 

37.
Schindler, D. W., Carpenter, S. R., Chapra, S. C., Hecky, R. E. & Orihel, D. M. Reducing phosphorus to curb lake eutrophication is a success. Environ. Sci. Technol. 50, 8923–8929 (2016).
CAS  PubMed  Article  PubMed Central  Google Scholar 

38.
Scheffer, M., Carpenter, S. R., Foley, J. E., Folke, C. & Walker, B. Catastrophic shifts in ecosystems. Nature 413, 591–596 (2001).
CAS  PubMed  Article  PubMed Central  Google Scholar 

39.
Hopf, J. K., Jones, G. P., Williamson, D. H. & Connolly, S. R. Fishery consequences of marine reserves: short-term pain for longer-term gain. Ecol. Appl. 26, 818–829 (2016).
PubMed  Article  Google Scholar 

40.
Hobbs, W. O. et al. A 200-year perspective on alternative stable state theory and lake management from a biomanipulated shallow lake. Ecol. Appl. 22, 1483–1496 (2012).
PubMed  Article  Google Scholar 

41.
Fastner, J. et al. Combating cyanobacterial proliferation by avoiding or treating inflows with high P load-experiences from eight case studies. Aquat. Ecol. 50, 367–383 (2016).
CAS  Article  Google Scholar 

42.
Vollenweider, R. A. Input-output models with special reference to the phosphorus loading concept in limnology. Schweiz. Z. Hydrol. 37, 53–84 (1975).
CAS  Google Scholar 

43.
Cullen, P. & Forsberg, C. Experiences with reducing point sources of phosphorus to lakes. Hydrobiologia 170, 321–336 (1988).
CAS  Article  Google Scholar 

44.
Jeppesen, E. et al. Lake responses to reduced nutrient loading – an analysis of contemporary long-term data from 35 case studies. Freshwat. Biol. 50, 1747–1771 (2005).
CAS  Article  Google Scholar 

45.
Carpenter, S. R. & Brock, W. A. Spatial complexity, resilience, and policy diversity: fishing on lake-rich landscapes. Ecol. Soc. 9, 8 (2004).
Article  Google Scholar 

46.
Walters, C. & Kitchell, J. F. Cultivation/depensation effects on juvenile survival and recruitment: implications for the theory of fishing. Can. J. Fish. Aquat. Sci. 58, 39–50 (2001).
Article  Google Scholar 

47.
Carpenter, S. R. Ecological futures: building an ecology of the long now. Ecology 83, 2069–2083 (2002).
Google Scholar 

48.
Carpenter, S. R. Regime Shifts in Lake Ecosystems: Pattern and Variation (Ecology Institute, 2003).

49.
Francis, T. B. & Schindler, D. E. Degradation of littoral habitats by residential development: woody debris in lakes of the Pacific Northwest and Midwest, United States. Ambio 35, 274–280 (2006).

50.
Christensen, D. L., Herwig, B. R., Schindler, D. E. & Carpenter, S. R. Impacts of lakeshore residential development on coarse woody debris in north temperate lakes. Ecol. Appl. 6, 1143–1149 (1996).
Article  Google Scholar 

51.
Grebogi, C., Ott, E. & Yorke, J. A. Crises, sudden changes in chaotic attractors and chaotic transients. Phys. D 7, 181–200 (1983).
Article  Google Scholar 

52.
Tél, T. in Directions in Chaos (3): Experimental Study and Characterization of Chaos (ed. Hao, B.-L.) 149–211 (World Scientific, 1990).

53.
Lai, Y.-C. & Tél, T. Transient Chaos: Complex Dynamics on Finite-Time Scales (Springer, 2011).

54.
McCann, K. S. & Yodzis, P. Nonlinear dynamics and population disappearances. Am. Nat. 144, 873–879 (1994).
Article  Google Scholar 

55.
Schiff, S. J. et al. Controlling chaos in the brain. Nature 370, 615–620 (1994).
CAS  PubMed  Article  Google Scholar 

56.
Dhamala, M. & Lai, Y.-C. Controlling transient chaos in deterministic flows with applications to electrical power systems and ecology. Phys. Rev. E 59, 1646–1655 (1999).
CAS  Article  Google Scholar 

57.
Hilker, F. M. & Westerhoff, F. H. Preventing extinction and outbreaks in chaotic populations. Am. Nat. 170, 232–241 (2007).
PubMed  Article  Google Scholar 

58.
Park, M.-G., Park, S.-A., Cho, K. & Jang, B. Controlling transient of species in food chain. Proc. Korean Ind. Appl. Math. Assoc. 6, 249–253 (2011).
Google Scholar 

59.
Tel, T. Controlling transient chaos. J. Phys. A 24, L1359–L1368 (1991).
Article  Google Scholar 

60.
Lai, Y.-C. & Grebogi, C. Converting transient chaos into sustained chaos by feedback control. Phys. Rev. E 49, 1094–1098 (1994).
CAS  Article  Google Scholar 

61.
Schwartz, I. B. & Triandaf, I. Sustaining chaos by using basin boundary saddles. Phys. Rev. Lett. 77, 4740–4743 (1996).
CAS  PubMed  Article  Google Scholar 

62.
Ott, E., Grebogi, C. & Yorke, J. A. Controlling chaos. Phys. Rev. Lett. 64, 1196–1199 (1990).
CAS  PubMed  Article  Google Scholar 

63.
Folke, C. et al. Resilience thinking: integrating resilience, adaptability and transformability. Ecol. Soc. 15, 20 (2010).
Article  Google Scholar 

64.
Walters, C. J. & Holling, C. S. Large-scale management experiments and learning by doing. Ecology 71, 2060–2068 (1990).
Article  Google Scholar 

65.
Bulman, C. R. et al. Minimum viable metapopulation size, extinction debt, and the conservation of a declining species. Ecol. Appl. 17, 1460–1473 (2007).
PubMed  Article  Google Scholar 

66.
Mcdonald, J. L., Stott, I., Townley, S. & Hodgson, D. J. Transients drive the demographic dynamics of plant populations in variable environments. J. Ecol. 104, 306–314 (2016).
PubMed  PubMed Central  Article  Google Scholar 

67.
Carpenter, S. R. & Gunderson, L. H. Coping with collapse: ecological and social dynamics in ecosystem management. Bioscience 51, 451–457 (2001).
Article  Google Scholar 

68.
Fulton, E. A. et al. A multi-model approach to engaging stakeholder and modellers in complex environmental problems. Environ. Sci. Policy 48, 44–56 (2015).
Article  Google Scholar 

69.
Plagányi, É. E. et al. Multispecies fisheries management and conservation: tactical applications using models of intermediate complexity. Fish Fish. 15, 1–22 (2014).
Article  Google Scholar 

70.
Collie, J. S. et al. Ecosystem models for fisheries management: finding the sweet spot. Fish Fish. 17, 101–125 (2016).
Article  Google Scholar 

71.
Rowland, J. A. et al. Selecting and applying indicators of ecosystem collapse for risk assessments. Conserv. Biol. 32, 1233–1245 (2018).
PubMed  Article  Google Scholar 

72.
Silvertown, J. et al. The Park Grass Experiment 1856–2006: its contribution to ecology. J. Ecol. 94, 801–814 (2006).
CAS  Article  Google Scholar 

73.
Pace, M. L., Carpenter, S. R. & Wilkinson, G. M. Long-term studies and reproducibility: lessons from whole-lake experiments. Limnol. Oceanogr. 64, S22–S33 (2019).
CAS  Article  Google Scholar 

74.
McGlathery, K. J. et al. Nonlinear dynamics and alternative stable states in shallow coastal systems. Oceanography 26, 220–231 (2013).
Article  Google Scholar 

75.
Van Cleve, K. & Martin, S. (eds) Long-Term Ecological Research in the United States: A Network of Research Sites 6th edn (Long Term Ecological Research Office, 1991).

76.
Bestelmeyer, B. T. et al. Analysis of abrupt transitions in ecological systems. Ecosphere https://doi.org/10.1890/ES11-00216.1 (2011).

77.
Reed-Andersen, T., Carpenter, S. R. & Lathrop, R. C. Phosphorus flow in a watershed-lake ecosystem. Ecosystems 3, 561–573 (2000).
CAS  Article  Google Scholar 

78.
Bell, D. M. et al. Long-term ecological research and evolving frameworks of disturbance ecology. BioScience 70, 141–156 (2020).
Article  Google Scholar 

79.
Pahl-Wostl, C. A conceptual framework for analysing adaptive capacity and multi-level learning processes in resource governance regimes. Glob. Environ. Change 19, 354–365 (2009).
Article  Google Scholar 

80.
White, J. W. et al. Transient responses of fished populations to marine reserve establishment. Conserv. Lett. 6, 180–191 (2013).
Article  Google Scholar 

81.
Chadès, I. et al. Optimization methods to solve adaptive management problems. Theor. Ecol. 10, 1–20 (2017).
Article  Google Scholar 

82.
Kot, M. Elements of Mathematical Ecology (Cambridge Univ. Press, 2001).

83.
Strogatz, S. H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering (Addison-Wesley, 1994). More

1.
Pan, Y. et al. A large and persistent carbon sink in the world’s forests. Science 333, 988–993 (2011).
CAS  PubMed  PubMed Central  Article  ADS  Google Scholar 
2.
Blenkinsop, S. & Fowler, H. J. Changes in drought frequency, severity and duration for the British Isles projected by the PRUDENCE regional climate models. J. Hydrol. 342, 50–71 (2007).
Article  ADS  Google Scholar 

3.
Guardiola-Claramonte, M. et al. Decreased streamflow in semi-arid basins following drought-induced tree die-off: a counter-intuitive and indirect climate impact on hydrology. J. Hydrol. 406, 225–233 (2011).
Article  ADS  Google Scholar 

4.
Hartmann, H. et al. Research frontiers for improving our understanding of drought-induced tree and forest mortality. New Phytol. 218, 15–28 (2018).
PubMed  Article  PubMed Central  Google Scholar 

5.
Chaturvedi, R. K., Raghubanshi, A. S., Tomlinson, K. & Singh, J. S. Impacts of human disturbance in tropical dry forests increase with soil moisture stress. J. Veg. Sci. 28, 997–1007 (2017).
Article  Google Scholar 

6.
Sjöman, H., Hirons, A. D. & Bassuk, N. L. Improving confidence in tree species selection for challenging urban sites: a role for leaf turgor loss. Urban Ecosyst. 21, 1171–1188 (2018).
Article  Google Scholar 

7.
Esperon-Rodriguez, M. et al. Assessing the vulnerability of Australia’s urban forests to climate extremes. Plants People Planet. 1, 387–397 (2019).
Article  Google Scholar 

8.
Thaiutsa, B., Puangchit, L., Kjelgren, R. & Arunpraparut, W. Urban green space, street tree and heritage large tree assessment in Bangkok, Thailand. Urban For. Urban Green. 7, 219–229 (2008).
Article  Google Scholar 

9.
Chaturvedi, R.K., Tripathi, A., Raghubanshi, A.S. & Singh, J.S. Functional traits indicate a continuum of treee drought strategies across a soil water availability gradient in a tropical dry forest. For. Ecol. Manag. 2020 (In press).

10.
Chaturvedi, R. K., Raghubanshi, A. S. & Singh, J. S. Growth of tree seedlings in a tropical dry forest in relation to soil moisture and leaf traits. J. Plant Ecol. 6, 158–170 (2013).
Article  Google Scholar 

11.
Krauss, K. W., Twilley, R. R., Doyle, T. W. & Gardiner, E. S. Leaf gas exchange characteristics of three neotropical mangrove species in response to varying hydroperiod. Tree Physiol. 26, 959–968 (2006).
PubMed  Article  PubMed Central  Google Scholar 

12.
Yan, M.-J., Yamanaka, N., Yamamoto, F. & Du, S. Responses of leaf gas exchange, water relations, and water consumption in seedlings of four semiarid tree species to soil drying. Acta Physiol. Plant. 32, 183–189 (2010).
Article  Google Scholar 

13.
Yan, W., Zheng, S., Zhong, Y. & Shangguan, Z. Contrasting dynamics of leaf potential and gas exchange during progressive drought cycles and recovery in Amorpha fruticosa and Robinia pseudoacacia. Sci. Rep. 7, 4470 (2017).
PubMed  PubMed Central  Article  ADS  CAS  Google Scholar 

14.
Medlyn, B. E. et al. Stomatal conductance of forest species after long-term exposure to elevated CO2 concentration: a synthesis. New Phytol. 149, 247–264 (2001).
Article  Google Scholar 

15.
Wullschleger, S. D., Gunderson, C. A., Hanson, P. J., Wilson, K. B. & Norby, R. J. Sensitivity of stomatal and canopy conductance to elevated CO2 concentration: interacting variables and perspectives of scale. New Phytol. 153, 485–496 (2002).
CAS  Article  Google Scholar 

16.
Ainsworth, E. A. & Rogers, A. The response of photosynthesis and stomatal conductance to rising [CO2]: mechanisms and environmental interactions. Plant. Cell Environ. 30, 258–270. https://doi.org/10.1111/j.1365-3040.2007.01641.x (2007).
CAS  Article  PubMed  Google Scholar 

17.
Tor-ngern, P. et al. Increases in atmospheric CO2 have little influence on transpiration of a temperate forest canopy. New Phytol. 205, 518–525 (2015).
CAS  PubMed  Article  Google Scholar 

18.
Schäfer, K. V. R. et al. Exposure to an enriched CO2 atmosphere alters carbon assimilation and allocation in a pine forest ecosystem. Glob. Chang. Biol. 9, 1378–1400 (2003).
Article  ADS  Google Scholar 

19.
Williams, M. et al. Modelling the soil-plant-atmosphere continuum in a Quercus-Acer stand at Harvard Forest: the regulation of stomatal conductance by light, nitrogen and soil/plant hydraulic properties. Plant. Cell Environ. 19, 911–927 (1996).
Article  Google Scholar 

20.
Granier, A. Une nouvelle méthode pour la mesure du flux de sève brute dans le tronc des arbres. Ann. For. Sci. 42, 193–200 (1985).
Article  Google Scholar 

21.
Granier, A. Evaluation of transpiration in a Douglas-fir stand by means of sap flow measurements. Tree Physiol. 3, 309–320 (1987).
CAS  PubMed  Article  Google Scholar 

22.
Green, S., Clothier, B. & Jardine, B. Theory and practical application of heat pulse to measure sap flow. Agron. J. 95, 1371–1379 (2003).
Article  Google Scholar 

23.
Burgess, S. S. O. et al. An improved heat pulse method to measure low and reverse rates of sap flow in woody plants. Tree Physiol. 21, 589–598 (2001).
CAS  PubMed  Article  PubMed Central  Google Scholar 

24.
Sakuratani, T. A Heat balance method for measuring water flux in the stem of intact plants. J. Agric. Meteorol. 37, 9–17 (1981).
Article  Google Scholar 

25.
Chang, X., Zhao, W., Zhang, Z. & Su, Y. Sap flow and tree conductance of shelter-belt in arid region of China. Agric. For. Meteorol. 138, 132–141 (2006).
Article  ADS  Google Scholar 

26.
Ewers, B. E., Oren, R., Phillips, N., Strömgren, M. & Linder, S. Mean canopy stomatal conductance responses to water and nutrient availabilities in Picea abies and Pinus taeda. Tree Physiol. 21, 841–850 (2001).
CAS  PubMed  Article  PubMed Central  Google Scholar 

27.
Pataki, D. E., Oren, R. & Phillips, N. Responses of sap flux and stomatal conductance of Pinus taeda L. trees to stepwise reductions in leaf area. J. Exp. Bot. 49, 871–878 (1998).
CAS  Article  Google Scholar 

28.
Ryan, M. G. et al. Transpiration and whole-tree conductance in ponderosa pine trees of different heights. Oecologia 124, 553–560 (2000).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

29.
Oishi, A. C., Oren, R., Novick, K. A., Palmroth, S. & Katul, G. G. Interannual invariability of forest evapotranspiration and its consequence to water flow downstream. Ecosystems 13, 421–436 (2010).
Article  Google Scholar 

30.
Oishi, A. C., Oren, R. & Stoy, P. C. Estimating components of forest evapotranspiration: a footprint approach for scaling sap flux measurements. Agric. For. Meteorol. 148, 1719–1732 (2008).
Article  ADS  Google Scholar 

31.
Bell, D. M. et al. A state-space modeling approach to estimating canopy conductance and associated uncertainties from sap flux density data. Tree Physiol. 35, 792–802 (2015).
PubMed  Article  PubMed Central  Google Scholar 

32.
Kim, H.-S., Oren, R. & Hinckley, T. M. Actual and potential transpiration and carbon assimilation in an irrigated poplar plantation. Tree Physiol. 28, 559–577 (2008).
CAS  PubMed  Article  PubMed Central  Google Scholar 

33.
Meinzer, F. C., James, S. A. & Goldstein, G. Dynamics of transpiration, sap flow and use of stored water in tropical forest canopy trees. Tree Physiol. 24, 901–909 (2004).
PubMed  Article  PubMed Central  Google Scholar 

34.
Phillips, N., Nagchaudhuri, A., Oren, R. & Katul, G. Time constant for water transport in loblolly pine trees estimated from time series of evaporative demand and stem sapflow. Trees 11, 412–419 (1997).
Article  Google Scholar 

35.
Tor-ngern, P. et al. Ecophysiological variation of transpiration of pine forests: synthesis of new and published results. Ecol. Appl. 27, 118–133 (2017).
PubMed  Article  PubMed Central  Google Scholar 

36.
Clark, J. S. et al. Inferential ecosystem models, from network data to prediction. Ecol. Appl. 21, 1523–1536 (2011).
PubMed  Article  PubMed Central  Google Scholar 

37.
Lu, P., Urban, L. & Zhao, P. Granier’s thermal dissipation probe (TDP) method for measuring sap flow in trees: theory and practice. Acta Bot. Sin. 46, 631–646 (2004).
Google Scholar 

38.
Ewers, B. & Oren, R. Analyses of assumptions and errors in the calculation of stomatal conductance from sap flux measurements. Tree Physiol. 20, 579–589 (2000).
PubMed  Article  PubMed Central  Google Scholar 

39.
Ward, E. J., Oren, R., Sigurdsson, B. D., Jarvis, P. G. & Linder, S. Fertilization effects on mean stomatal conductance are mediated through changes in the hydraulic attributes of mature Norway spruce trees. Tree Physiol. 28, 579–596 (2008).
PubMed  Article  PubMed Central  Google Scholar 

40.
Addington, R. N., Mitchell, R. J., Oren, R. & Donovan, L. A. Stomatal sensitivity to vapor pressure deficit and its relationship to hydraulic conductance in Pinus palustris. Tree Physiol. 24, 561–569 (2004).
PubMed  Article  Google Scholar 

41.
Leuning, R. A critical appraisal of a combined stomatal-photosynthesis model for C3 plants. Plant. Cell Environ. 18, 339–355 (1995).
CAS  Article  Google Scholar 

42.
Meinzer, F. C., Hinckley, T. M. & Ceulemans, R. Apparent responses of stomata to transpiration and humidity in a hybrid poplar canopy. Plant. Cell Environ. 20, 1301–1308 (1997).
Article  Google Scholar 

43.
Monteith, J. L. A reinterpretation of stomatal responses to humidity. Plant. Cell Environ. 18, 357–364 (1995).
Article  Google Scholar 

44.
Loustau, D. et al. Transpiration of a 64-year-old maritime pine stand in Portugal. Oecologia 107, 33–42 (1996).
CAS  PubMed  Article  ADS  Google Scholar 

45.
Domec, J.-C. & Gartner, B. L. Cavitation and water storage capacity in bole xylem segments of mature and young Douglas-fir trees. Trees 15, 204–214 (2001).
Article  Google Scholar 

46.
Moore, G. W., Bond, B. J., Jones, J. A., Phillips, N. & Meinzer, F. C. Structural and compositional controls on transpiration in 40- and 450-year-old riparian forests in western Oregon, USA. Tree Physiol. 24, 481–491 (2004).
PubMed  Article  Google Scholar 

47.
Leigh, A., Sevanto, S., Close, J. D. & Nicotra, A. B. The influence of leaf size and shape on leaf thermal dynamics: does theory hold up under natural conditions?. Plant. Cell Environ. 40, 237–248 (2017).
CAS  PubMed  Article  Google Scholar 

48.
Brodribb, T. J., Holbrook, N. M., Edwards, E. J. & Gutiérrez, M. V. Relations between stomatal closure, leaf turgor and xylem vulnerability in eight tropical dry forest trees. Plant. Cell Environ. 26, 443–450 (2003).
Article  Google Scholar 

49.
Choat, B., Ball, M., Luly, J., Donnelly, C. & Holtum, J. Seasonal patterns of leaf gas exchange and water relations in dry rain forest trees of contrasting leaf phenology. Tree Physiol. 26, 657–664 (2006).
PubMed  Article  PubMed Central  Google Scholar 

50.
Tor-ngern, P. & Puangchit, L. Effects of varying soil and atmospheric water deficit on water use characteristics of tropical street tree species. Urban For. Urban Green. 36, 76–83 (2018).
Article  Google Scholar 

51.
Jarvis, P. G. Transpiration and assimilation of tree and agricultural crops: the omega factor. In Attributes of Trees as Crop Plants (eds Cannel, M. G. R. & Jackson, J. E.) 460–480 (Institute of Terrestrial Ecology Huntingdon, UK, 1985).
Google Scholar 

52.
Marchin, R. M., Broadhead, A. A., Bostic, L. E., Dunn, R. R. & Hoffmann, W. A. Stomatal acclimation to vapour pressure deficit doubles transpiration of small tree seedlings with warming. Plant. Cell Environ. 39, 2221–2234 (2016).
CAS  PubMed  Article  PubMed Central  Google Scholar 

53.
Mahan, J. R. & Upchurch, D. R. Maintenance of constant leaf temperature by plants—I Hypothesis-limited homeothermy. Environ. Exp. Bot. 28, 351–357 (1988).
Article  Google Scholar 

54.
Schultz, H. R. Differences in hydraulic architecture account for near-isohydric and anisohydric behaviour of two field-grown Vitis vinifera L. cultivars during drought. Plant. Cell Environ. 26, 1393–1405 (2003).
Article  Google Scholar 

55.
Harris, P. P., Huntingford, C., Cox, P. M., Gash, J. H. C. & Malhi, Y. Effect of soil moisture on canopy conductance of Amazonian rainforest. Agric. For. Meteorol. 122, 215–227 (2004).
Article  ADS  Google Scholar 

56.
Kjelgren, R., Joyce, D. & Doley, D. Subtropical-tropical urban tree water relations and drought stress response strategies. Arboric. Urban For. 39, 125–131 (2013).
Google Scholar 

57.
West, A. G., Hultine, K. R., Jackson, T. L. & Ehleringer, J. R. Differential summer water use by Pinus edulis and Juniperus osteosperma reflects contrasting hydraulic characteristics. Tree Physiol. 27, 1711–1720 (2007).
CAS  PubMed  Article  PubMed Central  Google Scholar 

58.
Hatfield, J. L. & Prueger, J. H. Temperature extremes: effect on plant growth and development. Weather Clim. Extrem. 10, 4–10 (2015).
Article  Google Scholar 

59.
Suralta, R. R. & Yamauchi, A. Root growth, aerenchyma development, and oxygen transport in rice genotypes subjected to drought and waterlogging. Environ. Exp. Bot. 64, 75–82 (2008).
CAS  Article  Google Scholar 

60.
Lawler, J. J. et al. The scope and treatment of threats in endangered species recovery plans. Ecol. Appl. 12, 663–667 (2002).
Article  Google Scholar 

61.
Liu, H., Lin, J., Zhang, M., Lin, Z. & Wen, T. Extinction of poorest competitors and temporal heterogeneity of habitat destruction. Ecol. Modell. 219, 30–38 (2008).
Article  Google Scholar 

62.
Baltzer, J. L., Grégoire, D. M., Bunyavejchewin, S., Noor, N. S. M. & Davies, S. J. Coordination of foliar and wood anatomical traits contributes to tropical tree distributions and productivity along the Malay-Thai Peninsula. Am. J. Bot. 96, 2214–2223 (2009).
PubMed  Article  Google Scholar 

63.
Kursar, T. A. et al. Tolerance to low leaf water status of tropical tree seedlings is related to drought performance and distribution. Funct. Ecol. 23, 93–102 (2009).
Article  Google Scholar 

64.
Monteith, J. L. & Unsworth, M. H. Principles of Environmental Physics 287 (Butterworth-Heinemann, Oxford, 1990).
Google Scholar 

65.
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods. 9(7), 671–675 (2012).
CAS  PubMed  PubMed Central  Article  Google Scholar 

66.
Oishi, A. C., Hawthorne, D. A. & Oren, R. Baseliner: an open-source, interactive tool for processing sap flux data from thermal dissipation probes. Software X. 5, 139–143 (2016).
ADS  Google Scholar 

67.
Ball, J., Woodrow, I. & Berry, J. A model predicting stomatal conductance and its contribution to the control of photosynthesis under different environmental conditions. Prog. Photosynth. Res. 4, 221–224 (1987).
Google Scholar 

68.
Jarvis, P. G. The interpretation of the variations in leaf water potential and stomatal conductance found in canopies in the field. Philos. Trans. R. Soc. London. B Biol. Sci. 273, 593–610 (1976).
CAS  Article  ADS  Google Scholar  More

SST data
I used the National Oceanic and Atmospheric Administration (NOAA) daily optimum interpolation SST gridded dataset V2.0 to identify MHWs in the period 1 January 1982 to 31 December 20184,28. The dataset is a blend of observations from satellites, ships and buoys and includes bias adjustment of satellite and ship observations to compensate for platform differences and sensor biases. Remotely sensed SSTs were obtained through the Advanced Very High Resolution Radiometer and interpolated daily onto a 0.25° × 0.25° spatial grid globally. Data were provided by the NOAA/OAR/ESRL PSD, Boulder, Colorado, USA, from their Web site at https://www.esrl.noaa.gov/psd/ accessed in January 2019.
I also obtained data from simulation models implemented in the fifth phase of the Coupled Model Intercomparison Project (CMIP5). I used the first ensemble member r1i1p1 of 12 coupled Earth System Models that allowed the analysis of variation in daily SSTs in all scenarios: CNMR-CM5, GFDL-CM3, GFDL-ESM2G, GFDLESM2M, IPSL-CM5A-LR, IPSL-CM5A-MR, MPI-ESM-LR, MPI-ESM-MR, MIROC5, MIROC-ESM, MRI-CGCM3, MIROC-ESM-CHEM. A climatology (the statistical properties of the timeseries, including the mean, variance, seasonal cycle and quantiles; see section “Identifying marine heatwaves” below for derivation) was obtained from historical simulations over the period 1861–2005 and used to identify MHWs for the historical scenario and for simulated SSTs over the period 2006–2100 following high and low emission scenarios (RCP 8.5 and RCP 2.6, respectively; RCP, representative concentration pathway). All the analyses on simulated data were implemented on a multi-model ensemble obtained by averaging the twelve models, unless otherwise indicated. For comparisons with the simulated SSTs, the satellite 0.25° × 0.25° data were regridded by averaging daily onto a regular 1° × 1° grid. The climatology for the satellite MHWs was derived from the whole observational period (1982–2018).
Whether a fixed climatology is appropriate instead of using shifting baselines to define MHWs is a matter of debate13,40. Here, the historical scenario provides a common reference to gauge shifts in the spatiotemporal dynamics of projected MHWs under high (RCP 8.5) and low (RCP 2.6) emission scenarios.
Identifying marine heatwaves
I identified MHWs from daily observed and simulated SST timeseries within each 1° × 1° cell following Hobday et al.27, who define a MHW as an anomalously warm water event with daily SSTs exceeding the seasonally varying 90th percentile (climatological threshold) for at least 5 consecutive days. The climatological mean and threshold were computed for each calendar day within a 11-day window centered on the focal day across all years within the climatological period. The mean and threshold were further smoothed by applying a 31-day moving average. Two events with a break of less than 3 days were considered the same MHW. I then derived characteristic metrics of MHWs, including duration, intensity and frequency and linked them to network properties (see below, Network analysis). Only SST timeseries with less than 10% of missing data were used in the analysis. I used the R package heatwaveR to identify marine heatwaves from SSTs41.
Topological data analysis and the Mapper workflow
Topological Data Analysis (TDA) is a collection of statistical methods based on topology, the field of mathematics that deals with the study of shapes, to find structure in complex datasets24. The Mapper algorithm is one tool of TDA that allows reducing high-dimensional data into a combinatorial object that encapsulates the original topological and geometric information of the data, such that points close to each other are more similar than distant points. The combinatorial object, also called a shape graph, is indeed a network with nodes and edges. The statistical properties of the TDA-based Mapper algorithm and how it relates to other non-linear dimensionality reduction techniques have been discussed in Ref.22. Here, I briefly summarize the five key steps involved in a Mapper analysis (Fig. 1). The first step of MAPPER consists of collapsing a raster stack of spatiotemporal data of MHWs into a binary 2D matrix where rows are timeframes (days) and columns are 1° × 1° cells arranged sequentially to represent the occurrence of MHWs across the global ocean. The first column of the matrix corresponds to the upper-left pixel of the raster centered at 89.5°N and − 180°W and the subsequent 364 columns represent adjacent pixels within the same latitude. Column 366 is centered at 88.5°N and − 180°W and so on, with the last column of the matrix corresponding to the lower-right pixel at − 89.5°S and 180°E. Although this scheme would result in matrices with 64,800 columns (360 × 180), I used reduced matrices in computations by excluding pixels on land or where missing SST values prevented the identification of MHWs. The final size of the matrices used in the analysis is (rows × columns) 13,514 × 42,365 for observed SSTs and 52,960 × 41,968, 34,675 × 41,074 and 34,675 × 41,482 for simulated SSTs under the historical, RCP 2.6 and RCP 8.5 scenarios, respectively.
The second step of Mapper involves dimensionality reduction or filtering. I used the Uniform Manifold Approximation and Projection dimensionality reduction (UMAP) algorithm to perform nonlinear dimensionality reduction42. This algorithm is similar to t-distributed Stochastic Neighbor Embedding (tSNE), which is widely used in machine learning43. The advantage of UMAP is that it has superior run time performance compared to tSNE, while retaining the ability to preserve the local structure of the original high-dimensional space after projection into the low-dimensional space.
The third step of Mapper consists of dividing the output range generated by the filtering process into overlapping bins. The number of bins and the amount of overlap are determined by the resolution (R) and gain (G) parameters, respectively. I used an optimization procedure to objectivity identify the combination of parameters R and G that best localized timeframes with similar cumulative intensity of MHWs nearby in the network (see “Parameter search and sensitivity analysis”). This procedure selected R = 24 and G = 45 for observed SSTs and for the RCP 8.5 scenario, R = 22 and G = 45 for the historical scenario and R = 12 and G = 25 for the RCP 2.6 scenario.
The fourth step of Mapper consists of partial clustering of timeframes within bins. Although Mapper is flexible and can accommodate different clustering methods and distance functions, I employed single-linkage clustering with Euclidean distance25. It is worth noting that this approach does not involve averaging of timeframes within clusters, so the original information is preserved in a compressed representation of the data.
The fifth and final step involves the generation of the network graph from the low dimensional compressed representation of the data. Clusters become nodes in the network and nodes become connected if they share one or more timeframes. I implemented the TDA-based Mapper algorithm using a parallelized version of function mapper2D in the R package TDAmapper44.
Network analysis
I employed two widely used measures of network topology, modularity and node degree, to compare the structure of the four MHW networks. Modularity describes the strength of division of a network into communities—i.e. cohesive groups of nodes that have dense connections among them and that are only sparsely connected with nodes in other groups. High modularity indicates the presence of distinct regimes of spatiotemporal dynamics of MHWs. As a second measure of network structure, I used mean node degree—where the degree of a node is the number of edges that are incident to that node. High mean node degree indicates that many nodes share one or more timeframes and depicts similar spatiotemporal patterns of MHWs within those nodes. In contrast, low node degree indicates the occurrence of many isolated nodes with few timeframes in common and more isolated MHWs. I computed modularity and node degree with functions ‘modularity’ and ‘degree’ in the R package igraph45.
To provide significance tests for the observed measures of network topology and to evaluate if they originated simply from non-stationarity properties in the original data, I run two null models based on surrogate data for each of the four networks. Surrogate data can be obtained through the Fourier transform of the original timeseries, shuffling the phases and applying the inverse transform to generate the surrogate series46. Phase randomization preserves the power spectrum, autocorrelation function and other linear properties of the data, but not the amplitude distribution. To address this potential drawback, I generated surrogate timeseries via the Theiler’s Amplitude Adjusted Fourier Transform (AAFT) using function ‘surrogate’ in the R package fractal, which also preserves the amplitude distribution of the original timeseries47. Using this approach, I applied two schemes of randomization—one employing a random sequence for each timeseries and one employing the same sequence for all timeseries. Randomizing using a fixed sequence for all timeseries (constant phase) randomizes the nonlinear properties of the data while preserving linear properties, such as the linear cross-correlation function. The randomization scheme based on random sequences (random phase) also disrupts linear relationships in the data. A significant departure of the observed statistic from the null model under constant phase randomization allows rejecting the null hypothesis that the observed time series is a monotonic nonlinear transformation of a Gaussian process. A significant departure from the null model under random phase allows rejecting also the null hypothesis that the original data come from a linear Gaussian process. To assess significance, 1000 randomizations were performed for each network under each scheme of random and constant phase and a two-tailed test was performed at α = 0.025 to account for multiple testing (Bonferroni correction).
To quantify temporal transitions of MHWs, I estimated node degree of the temporal connectivity matrix (TCM) obtained from each network. The degree for each node in the TCM was estimated by counting the number of non-zero edges connected to that node22. Temporal fluctuations in node degree were benchmarked against the confidence intervals of the random phase null model, estimated as twice the standard deviation of the null distribution. A Generalized Additive Model (GAM) smooth function was fitted to node degree data to visualize temporal trends. The timing of collapse of node degree for the historical scenario was estimated as the year when the smooth curve intersected the upper confidence limit of the null model. To provide a measure of uncertainty, I obtained analogous estimates of the year of collapse by repeating the whole analysis for each of the twelve ESMs separately and computing the median and the bootstrap standard error (n = 1000) of these estimates. A similar analysis was done on the RCP 8.5 data to estimate the year when node degree increased again and diverged significantly from the null distribution. To determine the duration of the different period of connectivity identified in the TCMs, I used the change point algorithm implemented in function cpt.mean of package changepoint48.
Parameter search and sensitivity analysis
To objectively identify parameters R and G (resolution and gain) as part of the binning process in the Mapper algorithm, I used an optimization procedure that best localized timeframes with similar patterns of MHWs nearby in the network. Localization can be done for any of the properties of MHWs. I used cumulative intensity as the localization criterion since it was a good proxy for other properties of MHWs, such as duration (r = 0.88, p  More

Cross the line between air and water, and you enter a very different world. The air can be completely silent, but listen below the sea’s surface and your ears fill with sound.
Here, I’m listening to a colleague using a wireless acoustic signal to trigger the release of an underwater noise-monitoring buoy moored to the sea bed. When the buoy floats to the surface, we retrieve its data. It is one of nine being used to continuously record underwater noise for a year in the northern Adriatic Sea between Italy and Croatia. The devices are part of the Soundscape project, which launched in 2019 and is funded mainly by the European Commission.
Underwater noise was in the European Commission’s 2008 Marine Strategy Framework Directive for protecting the ocean environment. We know that noise can affect marine species, but no one has extensive baseline data on underwater sound levels. Soundscape aims to fill this knowledge gap by developing a planning tool for underwater noise management.
As a marine biologist, I monitor water quality and underwater noise around the Gulf of Trieste in the Adriatic. The gulf is a busy shipping area, so most of what we record is the low, continuous noise of ship traffic. But we can also hear the beating sounds of drum fish, the ‘pops’ of damsel fish as they communicate with partners, and the snapping claws of pistol shrimp.
Growing up by the sea, I was intrigued by all the sounds I could hear when I ducked beneath the waves. For my master’s thesis, colleagues and I recorded noise in the Gulf of Trieste and showed that the hearing sensitivity of fish there was reduced when we played them the recording in our laboratory. Now our main questions concern the effects of underwater noise at the population scale.
It’s sunny in this picture, and we try to organize monitoring around the best possible weather. But sometimes we just have to get wet. More

1.
Garrison, W. M., Morrison, D. C., Hamilton, J. G., Benson, A. A. & Calvin, M. Reduction of carbon dioxide in aqueous solutions by ionizing radiation. Science 114, 416–418 (1951).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 
2.
Draganić, Z. D., Draganić, I. G. & Borovičanin, M. The radiation chemistry of aqueous solutions of hydrogen cyanide in the megarad dose range. Radiat. Res. 66, 42–53 (1976).
PubMed  Article  ADS  PubMed Central  Google Scholar 

3.
Bar-Nun, A. & Hartman, H. Synthesis of organic compounds from carbon monoxide and water by UV photolysis. Origins Life 9, 93–101 (1978).
CAS  Article  ADS  Google Scholar 

4.
Miller, S. L. & Urey, H. C. Organic compound synthesis on the primitive earth. Science 130, 245–251 (1959).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

5.
Pasek, M. A., Dworkin, J. P. & Lauretta, D. S. A radical pathway for organic phosphorylation during schreibersite corrosion with implications for the origin of life. Geochim. Cosmochim. Acta 71, 1721–1736 (2007).
CAS  Article  ADS  Google Scholar 

6.
Lim, R. W. J. & Fahrenbach, A. C. Radicals in prebiotic chemistry. Pure Appl. Chem. 92, 1971–1986 (2020).
CAS  Article  Google Scholar 

7.
Studer, A. & Curran, D. P. Catalysis of radical reactions: A radical chemistry perspective. Angew. Chem. Int. Ed. 55, 58–102 (2016).
CAS  Article  Google Scholar 

8.
Shock, E. L. et al. Quantifying inorganic sources of geochemical energy in hydrothermal ecosystems, Yellowstone National Park, USA. Geochim. Cosmochim. Acta 74, 4005–4043 (2010).
CAS  Article  ADS  Google Scholar 

9.
Bím, D., Maldonado-Domínguez, M., Rulíšek, L. & Srnec, M. Beyond the classical thermodynamic contributions to hydrogen atom abstraction reactivity. Proc. Natl. Acad. Sci. USA 115, E10287–E10294 (2018).
PubMed  Article  CAS  PubMed Central  Google Scholar 

10.
Mayer, J. M. Hydrogen atom abstraction by metal–oxo complexes: Understanding the analogy with organic radical reactions. Acc. Chem. Res. 31, 441–450 (1998).
CAS  Article  Google Scholar 

11.
Gutowski, M. & Kowalczyk, S. A study of free radical chemistry: Their role and pathophysiological significance. Acta Biochim. Pol. 60, 1–16 (2013).
CAS  PubMed  Article  PubMed Central  Google Scholar 

12.
Moran, J. & Rauscher, S. Energy and self-organization at the origin of metabolism. Commun. Chem. (in rev.).

13.
Nghe, P. et al. Prebiotic network evolution: Six key parameters. Mol. BioSyst. 11, 3206–3217 (2015).
CAS  PubMed  Article  PubMed Central  Google Scholar 

14.
Jolley, C. & Douglas, T. Topological biosignatures: Large-scale structure of chemical networks from biology and astrochemistry. Astrobiology 12, 29–39 (2012).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

15.
Solé, R. V. & Munteanu, A. The large-scale organization of chemical reaction networks in astrophysics. Europhys. Lett. 68, 170–176 (2004).
Article  ADS  CAS  Google Scholar 

16.
Shenhav, B., Solomon, A., Lancet, D. & Kafri, R. in Transactions on Computational Systems Biology I (ed. Priami, C.) 14–27 (Springer, Berlin, 2005).
Google Scholar 

17.
Brown, J. H. et al. The fractal nature of nature: Power laws, ecological complexity and biodiversity. Philos. Trans. R. Soc. Lond. B 357, 619–626 (2002).
Article  Google Scholar 

18.
Walker, S. I. & Mathis, C. in Prebiotic Chemistry and Chemical Evolution of Nucleic Acids (ed. Menor-Salvár, C.) 263–291 (Springer, Berlin, 2018).
Google Scholar 

19.
Hordijk, W., Hein, J. & Steel, M. Autocatalytic sets and the origin of life. Entropy 12, 1733–1742 (2010).
CAS  Article  ADS  Google Scholar 

20.
Albert, R. Scale-free networks in cell biology. J. Cell. Sci. 118, 4947–4957 (2005).
CAS  PubMed  Article  PubMed Central  Google Scholar 

21.
Liu, R., Mao, G. & Zhang, N. Research of chemical elements and chemical bonds from the view of complex network. Found. Chem. 21, 193–206 (2019).
CAS  Article  Google Scholar 

22.
Estrada, E. The complex networks of earth minerals and chemical elements. MATCH Commun. Math. Comput. Chem. 59, 605–624 (2008).
MathSciNet  CAS  MATH  Google Scholar 

23.
Fricker, M. D., Boddy, L., Nakagaki, T. & Bebber, D. P. In Adaptive Biological Networks (eds. Gross, T. & Sayama, H.) 51–70 (Springer, Berlin, 2009).
Google Scholar 

24.
Nicolis, G. Chemical chaos and self-organization. J. Phys. Condens. Matter 2, SA47–SA62 (1990).
CAS  Article  ADS  Google Scholar 

25.
Pérez-Mercader, J. In Astrobiology (eds. Horneck, G. & Baumstark-Khan, C.) 337–360 (Springer, Berlin, 2002).
Google Scholar 

26.
Li, W. Expansion-modification systems: A model for spatial 1/f spectra. Phys. Rev. A 43, 5240–5260 (1991).
MathSciNet  CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

27.
Albert, R. & Barabási, A.-L. Topology of evolving networks: Local events and universality. Phys. Rev. Lett. 85, 5234–5237 (2000).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

28.
Barabási, A.-L. & Albert, R. Emergence of scaling in random networks. Science 286, 509–512 (1999).
MathSciNet  PubMed  MATH  Article  ADS  PubMed Central  Google Scholar 

29.
Marković, D. & Gros, C. Power laws and self-organized criticality in theory and nature. Phys. Rep. 536, 41–74 (2014).
MathSciNet  Article  ADS  Google Scholar 

30.
Adler, R., Feldman, R. & Taqqu, M. (eds.) A Practical Guide to Heavy Tails: Statistical Techniques and Applications (Springer, Berlin, 1998).
Google Scholar 

31.
Patten, B. C. & Higashi, M. Modified cycling index for ecological applications. Ecol. Modell. 25, 69–83 (1984).
Article  Google Scholar 

32.
Essington, T. E. & Carpenter, S. R. Nutrient cycling in lakes and streams: Insights from a comparative analysis. Ecosystems 3, 131–143 (2000).
CAS  Article  Google Scholar 

33.
Christian, R. R. & Thomas, C. R. Network analysis of nitrogen inputs and cycling in the Neuse River estuary, North Carolina, USA. Estuaries 26, 815–828 (2003).
CAS  Article  Google Scholar 

34.
Allesina, S. & Ulanowicz, R. E. Cycling in ecological networks: Finn’s index revisited. Comput. Biol. Chem. 28, 227–233 (2004).
CAS  PubMed  MATH  Article  PubMed Central  Google Scholar 

35.
Loreau, M. Material cycling and the stability of ecosystems. Am. Nat. 143, 508–513 (1994).
Article  Google Scholar 

36.
DeAngelis, D. L. et al. Nutrient dynamics and food-web stability. Annu. Rev. Ecol. Syst. 20, 71–95 (1989).
Article  Google Scholar 

37.
Artzy-Randrup, Y. & Stone, L. Connectivity, cycles, and persistence thresholds in metapopulation networks. PLoS Comput. Biol. 6, e1000876 (2010).
MathSciNet  PubMed  PubMed Central  Article  ADS  CAS  Google Scholar 

38.
Newsholme, E. A. & Crabtree, B. Substrate cycles in metabolic regulation and in heat generation. Biochem. Soc. Symp. 41, 61–109 (1976).
CAS  Google Scholar 

39.
Kritz, M. V., dos Santos, M. T., Urrutia, S. & Schwartz, J.-M. Organising metabolic networks: Cycles in flux distributions. J. Theor. Biol. 265, 250–260 (2010).
MathSciNet  PubMed  MATH  Article  PubMed Central  Google Scholar 

40.
Valentine, J. W. & May, C. L. Hierarchies in biology and paleontology. Paleobiology 22, 23–33 (1996).
Article  Google Scholar 

41.
McShea, D. W. The hierarchical structure of organisms: A scale and documentation of a trend in the maximum. Paleobiology 27, 405–423 (2001).
Article  Google Scholar 

42.
Trebilco, R., Baum, J. K., Salomon, A. K. & Dulvy, N. K. Ecosystem ecology: Size-based constraints on the pyramids of life. Trends Ecol. Evol. 28, 423–431 (2013).
PubMed  Article  PubMed Central  Google Scholar 

43.
Lindeman, R. L. The trophic-dynamic aspect of ecology. Bull. Math. Biol. 53, 167–191 (1991).
Article  Google Scholar 

44.
Kleidon, A. & Lorenz, R. D. (eds.) Non-equilibrium Thermodynamics and the Production of Entropy: Life, Earth, and Beyond (Springer, Berlin, 2005).
Google Scholar 

45.
Goldenfeld, N. & Woese, C. Life is physics: Evolution as a collective phenomenon far from equilibrium. Annu. Rev. Condens. Matter Phys. 2, 375–399 (2011).
CAS  Article  ADS  Google Scholar 

46.
Braakman, R. & Smith, E. The compositional and evolutionary logic of metabolism. Phys. Biol. 10, 011001 (2013).
PubMed  Article  ADS  CAS  PubMed Central  Google Scholar 

47.
Ji, S. Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and Biomedical Applications (Springer, Berlin, 2012).
Google Scholar 

48.
Yi, R. et al. A continuous reaction network that produces RNA precursors. Proc. Natl. Acad. Sci. USA 117, 13267–13274 (2020).
CAS  PubMed  Article  PubMed Central  Google Scholar 

49.
Yi, R., Hongo, Y., Yoda, I., Adam, Z. R. & Fahrenbach, A. C. Radiolytic synthesis of cyanogen chloride, cyanamide and simple sugar precursors. ChemistrySelect 3, 10169–10174 (2018).
CAS  Article  Google Scholar 

50.
Ritson, D. & Sutherland, J. D. Prebiotic synthesis of simple sugars by photoredox systems chemistry. Nat. Chem. 4, 895–899 (2012).
CAS  PubMed  PubMed Central  Article  Google Scholar 

51.
Ferus, M. et al. High energy radical chemistry formation of HCN-rich atmospheres on early Earth. Sci. Rep. 7, 6275 (2017).
PubMed  PubMed Central  Article  ADS  CAS  Google Scholar 

52.
Getoff, N. Significance of solvated electrons (eaq−) as promoters of life on Earth. In Vivo 28, 61–66 (2014).
CAS  PubMed  PubMed Central  Google Scholar 

53.
Negrón-Mendoza, A., Draganić, Z. D., Navarro-González, R. & Draganić, I. G. Aldehydes, ketones, and carboxylic acids formed radiolytically in aqueous solutions of cyanides and simple nitriles. Radiat. Res. 95, 248–261 (1983).
Article  ADS  Google Scholar 

54.
Adam, Z. R. et al. Estimating the capacity for production of formamide by radioactive minerals on the prebiotic Earth. Sci. Rep. 8, 265 (2018).
PubMed  PubMed Central  Article  ADS  CAS  Google Scholar 

55.
Bedau, M. A. et al. Open problems in artificial life. Artif. Life 6, 363–376 (2000).
CAS  PubMed  Article  PubMed Central  Google Scholar 

56.
Grassberger, P. in Information Dynamics NATO ASI Series (Series B: Physics) (eds. Atmanspacher, H. & Scheingraber, H.) 15–33 (Springer, Berlin, 1991).
Google Scholar 

57.
Kaneko, K. Chaos as a source of complexity and diversity in evolution. Artif. Life 1, 163–177 (1993).
Article  Google Scholar 

58.
Buhl, D. & Ponnamperuma, C. Interstellar molecules and the origin of life. Sp. Life Sci. 3, 157–164 (1971).
CAS  ADS  Google Scholar 

59.
Airapetian, V. S., Glocer, A., Gronoff, G., Hébrard, E. & Danchi, W. Prebiotic chemistry and atmospheric warming of early Earth by an active young Sun. Nat. Geosci. 9, 452–455 (2016).
CAS  Article  ADS  Google Scholar 

60.
Paranicas, C., Cooper, J. F., Garrett, H. B., Johnson, R. E. & Sturner, S. J. in Europa (eds. Pappalardo, R. T. et al.) 529–544 (University of Arizona Press, Tucson, 2009).
Google Scholar 

61.
Takano, Y., Masuda, H., Kaneko, T. & Kobayashi, K. Formation of amino acids from possible interstellar media by γ-rays and UV irradiation. Chem. Lett. 31, 986–987 (2002).
Article  Google Scholar 

62.
Powner, M. W., Gerland, B. & Sutherland, J. D. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459, 239–242 (2009).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

63.
Clauset, A., Shalizi, C. R. & Newman, M. E. J. Power-law distributions in empirical data. SIAM Rev. 51, 661–703 (2009).
MathSciNet  MATH  Article  ADS  Google Scholar 

64.
Grohe, M. in Proceedings of the 39th ACM SIGMOD-SIGACT-SIGAI Symposium on Principles of Database Systems 1–16 (Portland, OR, USA, 2020).

65.
Grover, A. & Leskovec, J. in Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 855–864 (San Francisco, CA, USA, 2016).

66.
Palumbo, E. et al. in The Semantic Web: European Semantic Web Conference Vol. 11155, 117–120 (Springer, Crete, Greece, 2018).

67.
Kim, M., Baek, S. H. & Song, M. Relation extraction for biological pathway construction using node2vec. BMC Bioinform. 19, 206 (2018).
Article  CAS  Google Scholar 

68.
Shen, Z., Chen, F., Yang, L. & Wu, J. Node2vec representation for clustering journals and as a possible measure of diversity. J. Data Inf. Sci. 4, 79–92 (2019).
Google Scholar 

69.
Barabási, A.-L. & Oltvai, Z. N. Network biology: Understanding the cell’s functional organization. Nat. Rev. Genet. 5, 101–113 (2004).
PubMed  Article  CAS  PubMed Central  Google Scholar 

70.
Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabási, A.-L. The large-scale organization of metabolic networks. Nature 407, 651–654 (2000).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

71.
Ritson, D. J. & Sutherland, J. D. Synthesis of aldehydic ribonucleotide and amino acid precursors by photoredox chemistry. Angew. Chem. Int. Ed. 52, 5845–5847 (2013).
CAS  Article  Google Scholar 

72.
Fahrenbach, A. C. et al. Common and potentially prebiotic origin for precursors of nucleotide synthesis and activation. J. Am. Chem. Soc. 139, 8780–8783 (2017).
CAS  PubMed  PubMed Central  Article  Google Scholar 

73.
Muñoz, M. A. Colloquium: Criticality and dynamical scaling in living systems. Rev. Mod. Phys. 90, 031001 (2018).
MathSciNet  Article  ADS  Google Scholar 

74.
Langton, C. G. Computation at the edge of chaos: Phase transitions and emergent computation. Phys. D Nonlinear Phenom. 42, 12–37 (1990).
MathSciNet  Article  ADS  Google Scholar 

75.
Bak, P., Tang, C. & Wiesenfeld, K. Self-organized criticality: An explanation of the 1/f noise. Phys. Rev. Lett. 59, 381–384 (1987).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

76.
Gaveau, B., Moreau, M. & Toth, J. Scenarios for self-organized criticality in dynamical systems. Open Syst. Inf. Dyn. 7, 297–308 (2000).
MathSciNet  MATH  Article  Google Scholar 

77.
Bak, P. & Paczuski, M. Complexity, contingency, and criticality. Proc. Natl. Acad. Sci. USA 92, 6689–6696 (1995).
CAS  PubMed  Article  ADS  PubMed Central  Google Scholar 

78.
Hoffmann, H. & Payton, D. W. Optimization by self-organized criticality. Sci. Rep. 8, 2358 (2018).
PubMed  PubMed Central  Article  ADS  CAS  Google Scholar 

79.
Lovecchio, E., Allegrini, P., Geneston, E., West, B. J. & Grigolini, P. From self-organized to extended criticality. Front. Physiol. 3, 98 (2012).
PubMed  PubMed Central  Article  Google Scholar 

80.
Lima-Mendez, G. & van Helden, J. The powerful law of the power law and other myths in network biology. Mol. BioSyst. 5, 1482–1493 (2009).
CAS  PubMed  Article  PubMed Central  Google Scholar 

81.
Broido, A. D. & Clauset, A. Scale-free networks are rare. Nat. Commun. 10, 1017 (2019).
Article  ADS  CAS  Google Scholar 

82.
Stumpf, M. P. H. & Porter, M. A. Critical truths about power laws. Science 335, 665–666 (2012).
MathSciNet  CAS  PubMed  MATH  Article  ADS  PubMed Central  Google Scholar 

83.
Mitzenmacher, M. A brief history of generative models for power law and lognormal distributions. Internet Math. 1, 226–251 (2003).
MathSciNet  MATH  Article  Google Scholar 

84.
Glassman, I., Yetter, R. A. & Glumac, N. G. Combustion 41–69 (Elsevier, New York, 2015).
Google Scholar 

85.
Gleiss, P. M., Stadler, P. F., Wagner, A. & Fell, D. A. Relevant cycles in chemical reaction networks. Adv. Complex Syst. 4, 207–226 (2001).
MathSciNet  MATH  Article  Google Scholar 

86.
Dančík, V., Basu, A. & Clemons, P. in Systems Biology (eds. Prokop, A. & Csukas, B.) 129–178 (Springer, Berlin, 2013).
Google Scholar 

87.
Patten, B. C., Higashi, M. & Burns, T. P. Trophic dynamics in ecosystem networks: Significance of cycles and storage. Ecol. Modell. 51, 1–28 (1990).
Article  Google Scholar 

88.
Orgel, L. E. The implausibility of metabolic cycles on the prebiotic Earth. PLoS Biol. 6, e18 (2008).
PubMed  PubMed Central  Article  CAS  Google Scholar 

89.
Monks, P. S. Gas-phase radical chemistry in the troposphere. Chem. Soc. Rev. 34, 376–395 (2005).
CAS  PubMed  Article  PubMed Central  Google Scholar 

90.
Platt, U. et al. in Tropospheric Chemistry: Results of the German Tropospheric Chemistry Programme (eds. Seiler, W. et al.) 359–394 (Springer, Berlin, 2002).
Google Scholar 

91.
Vasas, V., Fernando, C., Santos, M., Kauffman, S. & Szathmáry, E. Evolution before genes. Biol. Direct 7, 1 (2012).
PubMed  PubMed Central  Article  Google Scholar 

92.
Robertson, M. P. & Joyce, G. F. The origins of the RNA world. Cold Spring Harb. Perspect. Biol. 4, a003608 (2012).
PubMed  PubMed Central  Article  CAS  Google Scholar 

93.
Damer, B. & Deamer, D. The hot spring hypothesis for an origin of life. Astrobiology 20, 429–452 (2020).
PubMed  PubMed Central  Article  ADS  Google Scholar 

94.
Martin, W., Baross, J., Kelley, D. & Russell, M. J. Hydrothermal vents and the origin of life. Nat. Rev. Microbiol. 6, 805–814 (2008).
CAS  PubMed  Article  PubMed Central  Google Scholar 

95.
Soloveichik, D., Cook, M., Winfree, E. & Bruck, J. Computation with finite stochastic chemical reaction networks. Nat. Comput. 7, 615–633 (2008).
MathSciNet  MATH  Article  Google Scholar 

96.
Bastian, M., Heymann, S. & Jacomy, M. in Proceedings of the Third International AAAI Conference on Weblogs and Social Media 361–362 (2009).

97.
Alstott, J., Bullmore, E. & Plenz, D. powerlaw: A Python package for analysis of heavy-tailed distributions. PLoS One 9, e85777 (2014).
PubMed  PubMed Central  Article  ADS  CAS  Google Scholar  More

1.
Steffen, W. et al. Trajectories of the Earth System in the Anthropocene. Proc. Natl Acad. Sci. USA 115, 8252–8259 (2018).
CAS  PubMed  Article  Google Scholar 
2.
Crutzen, P. J. Geology of mankind. Nature 415, 23 (2002).
CAS  PubMed  Article  Google Scholar 

3.
Foley, J. A. et al. Global consequences of land use. Science 309, 570–574 (2005).
CAS  PubMed  PubMed Central  Article  Google Scholar 

4.
Kopp, R. E., Kirschvink, J. L., Hilburn, I. A. & Nash, C. Z. The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis. Proc. Natl Acad. Sci. USA 102, 11131–11136 (2005).
CAS  PubMed  Article  Google Scholar 

5.
Schirrmeister, B. E., de Vos, J. M., Antonelli, A. & Bagheri, H. C. Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proc. Natl Acad. Sci. USA 110, 1791–1796 (2013).
CAS  PubMed  Article  Google Scholar 

6.
Bennett, E. M. et al. Bright spots: seeds of a good Anthropocene. Front. Ecol. Environ. 14, 441–448 (2016).
Article  Google Scholar 

7.
Braje, T. J. Earth systems, human agency, and the Anthropocene: Planet Earth in the human age. J. Archaeol. Res. 23, 369–396 (2015).
Article  Google Scholar 

8.
Rick, T. C. & Sandweiss, D. H. Archaeology, climate, and global change in the age of humans. Proc. Natl Acad. Sci. USA 117, 8250–8253 (2020).
CAS  PubMed  Article  Google Scholar 

9.
Sabloff, J. A. Archaeology Matters: Action Archaeology in the Modern World (Routledge, 2008).

10.
Guttmann-Bond, E. Sustainability out of the past: how archaeology can save the planet. World Archaeol. 42, 355–366 (2010).
Article  Google Scholar 

11.
Reed, K. & Ryan, P. Lessons from the past and the future of food. World Archaeol. 51, 1–16 (2019).
Article  Google Scholar 

12.
Isendahl, C. & Stump, D. (eds) The Oxford Handbook of Historical Ecology and Applied Archaeology (Oxford Univ. Press, 2019).

13.
Fisher, C. Archaeology for sustainable agriculture. J. Archaeol. Res. 28, 393–441 (2019).
Article  Google Scholar 

14.
Wolverton, S. & Lyman, R. L. (eds) Conservation Biology and Applied Zooarchaeology (Univ. Arizona Press, 2012).

15.
Folke, C. Resilience: the emergence of a perspective for social-ecological systems analyses. Glob. Environ. Change 16, 253–267 (2006).
Article  Google Scholar 

16.
Raymond, H. The ecologically noble savage debate. Annu. Rev. Anthropol. 36, 177–190 (2007).
Article  Google Scholar 

17.
Steffen, W., Grinevald, J., Crutzen, P. J. & McNeill, J. R. The Anthropocene: conceptual and historical perspectives. Philos. Trans. R. Soc. Lond. A 369, 842–867 (2011).
Google Scholar 

18.
Ellis, E., Maslin, M., Boivin, N. & Bauer, A. A. Involve social scientists in defining the Anthropocene. Nature 540, 192–193 (2016).
Article  Google Scholar 

19.
Smith, B. D. & Zeder, M. A. The onset of the Anthropocene. Anthropocene 4, 8–13 (2013).
Article  Google Scholar 

20.
Lewis, S. L. & Maslin, M. Defining the Anthropocene. Nature 519, 171–180 (2015).
CAS  PubMed  Article  PubMed Central  Google Scholar 

21.
Boivin, N. et al. Ecological consequences of human niche construction: examining long-term anthropogenic shaping of global species distributions. Proc. Natl Acad. Sci. USA 113, 6388–6396 (2016).
CAS  PubMed  Article  PubMed Central  Google Scholar 

22.
Butchart, S. H. M. et al. Global biodiversity: indicators of recent declines. Science 328, 1164–1168 (2010).
CAS  PubMed  Article  PubMed Central  Google Scholar 

23.
Newbold, T. et al. Global effects of land use on local terrestrial biodiversity. Nature 520, 45–50 (2015).
CAS  PubMed  Article  PubMed Central  Google Scholar 

24.
Barnosky, A. D. et al. Has the Earth’s sixth mass extinction already arrived? Nature 471, 51–57 (2011).
CAS  PubMed  Article  PubMed Central  Google Scholar 

25.
Braje, T. J. & Erlandson, J. M. Human acceleration of animal and plant extinctions: a Late Pleistocene, Holocene, and Anthropocene continuum. Anthropocene 4, 14–23 (2013).
Article  Google Scholar 

26.
Haines-Young, R. & Potschin, M. in Ecosystem Ecology: A New Synthesis (eds Raffaelli, D. G. & Frid, C. L. J.) 110–139 (Cambridge Univ. Press, 2010).

27.
Foster, D. et al. The importance of land-use legacies to ecology and conservation. BioScience 53, 77–88 (2003).
Article  Google Scholar 

28.
Willis, K. J. & Birks, H. J. B. What is natural? The need for a long-term perspective in biodiversity conservation. Science 314, 1261–1265 (2006).
CAS  PubMed  Article  PubMed Central  Google Scholar 

29.
Dietl, G. P. & Flessa, K. W. Conservation paleobiology: putting the dead to work. Trends Ecol. Evol. 26, 30–37 (2011).
PubMed  Article  PubMed Central  Google Scholar 

30.
Szabó, P. & Hédl, R. Advancing the integration of history and ecology for conservation. Conserv. Biol. 25, 680–687 (2011).
PubMed  Article  PubMed Central  Google Scholar 

31.
Scharf, E. A. Deep time: the emerging role of archaeology in landscape ecology. Landsc. Ecol. 29, 563–569 (2014).
Article  Google Scholar 

32.
Dietl, G. P. et al. Conservation paleobiology: leveraging knowledge of the past to inform conservation and restoration. Annu. Rev. Earth Planet. Sci. 43, 79–103 (2015).
CAS  Article  Google Scholar 

33.
Whitlock, C., Colombaroli, D., Conedera, M. & Tinner, W. Land‐use history as a guide for forest conservation and management. Conserv. Biol. 32, 84–97 (2018).
PubMed  Article  PubMed Central  Google Scholar 

34.
Frazier, J. Sustainable use of wildlife: the view from archaeozoology. Nat. Conserv. 15, 163–173 (2007).
Article  Google Scholar 

35.
Lyman, R. L. A warrant for applied palaeozoology. Biol. Rev. 87, 513–525 (2012).
PubMed  Article  PubMed Central  Google Scholar 

36.
Braje, T. & Rick, T. C. From forest fires to fisheries management: anthropology, conservation biology, and historical ecology. Evol. Anthropol. 22, 303–311 (2013).
PubMed  Article  PubMed Central  Google Scholar 

37.
Rick, T. C. & Lockwood, R. Integrating paleobiology, archeology, and history to inform biological conservation. Conserv. Biol. 27, 45–54 (2013).
PubMed  Article  PubMed Central  Google Scholar 

38.
Barak, R. S. et al. Taking the long view: integrating recorded, archeological, paleoecological, and evolutionary data into ecological restoration. Int. J. Plant Sci. 177, 90–102 (2016).
Article  Google Scholar 

39.
Lambrides, A. B. & Weisler, M. I. Pacific Islands ichthyoarchaeology: implications for the development of prehistoric fishing studies and global sustainability. J. Archaeol. Res. 24, 275–324 (2016).
Article  Google Scholar 

40.
Foster, T., Olsen, L., Dale, V. & Cohen, A. Studying the past for the future: managing modern biodiversity from historic and prehistoric data. Hum. Organ. 69, 149–157 (2010).
Article  Google Scholar 

41.
Wilmshurst, J. M. et al. Use of pollen and ancient DNA as conservation baselines for offshore islands in New Zealand. Conserv. Biol. 28, 202–212 (2014).
PubMed  Article  PubMed Central  Google Scholar 

42.
Nogué, S. et al. Island biodiversity conservation needs palaeoecology. Nat. Ecol. Evol. 1, 0181 (2017).
Article  Google Scholar 

43.
Willis, K. J., Bailey, R. M., Bhagwat, S. A. & Birks, H. J. B. Biodiversity baselines, thresholds and resilience: testing predictions and assumptions using palaeoecological data. Trends Ecol. Evol. 25, 583–591 (2010).
CAS  PubMed  Article  PubMed Central  Google Scholar 

44.
Newsome, S. D. et al. The shifting baseline of northern fur seal ecology in the northeast Pacific Ocean. Proc. Natl Acad. Sci. USA 104, 9709–9714 (2007).
CAS  PubMed  Article  PubMed Central  Google Scholar 

45.
Szpak, P., Orchard, T., McKechnie, I. & Gröcke, D. Historical ecology of late Holocene sea otters (Enhydra lutris) from northern British Columbia: isotopic and zooarchaeological perspectives. J. Archaeol. Sci. 39, 1553–1571 (2012).
Article  Google Scholar 

46.
McCune, J. L., Pellatt, M. G. & Vellend, M. Multidisciplinary synthesis of long-term human–ecosystem interactions: a perspective from the Garry oak ecosystem of British Columbia. Biol. Conserv. 166, 293–300 (2013).
Article  Google Scholar 

47.
Jackson, S. T. & Hobbs, R. J. Ecological restoration in the light of ecological history. Science 325, 567–569 (2009).
CAS  PubMed  Article  PubMed Central  Google Scholar 

48.
Corlett, R. T. The shifted baseline: prehistoric defaunation in the tropics and its consequences for biodiversity conservation. Biol. Conserv. 163, 13–21 (2013).
Article  Google Scholar 

49.
Hofman, C. A. & Rick, T. C. Ancient biological invasions and island ecosystems: tracking translocations of wild plants and animals. J. Archaeol. Res. 26, 65–115 (2018).
Article  Google Scholar 

50.
Speller, C. F. et al. High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation. PLoS ONE 7, e51122 (2012).
CAS  PubMed  PubMed Central  Article  Google Scholar 

51.
Hofman, C. A., Rick, T. C., Fleischer, R. C. & Maldonado, J. E. Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends Ecol. Evol. 30, 540–549 (2015).
PubMed  Article  PubMed Central  Google Scholar 

52.
Waters, J. M. & Grosser, S. Managing shifting species: ancient DNA reveals conservation conundrums in a dynamic world. BioEssays 38, 1177–1184 (2016).
CAS  PubMed  Article  PubMed Central  Google Scholar 

53.
Valentine, K. et al. Ancient DNA reveals genotypic relationships among Oregon populations of the sea otter (Enhydra lutris). Conserv. Genet. 9, 933–938 (2008).
Article  Google Scholar 

54.
Newsome, S. D. et al. Pleistocene to historic shifts in bald eagle diets on the Channel Islands, California. Proc. Natl Acad. Sci. USA 107, 9246–9251 (2010).
CAS  PubMed  Article  PubMed Central  Google Scholar 

55.
Guiry, E. J. et al. Lake Ontario salmon (Salmo salar) were not migratory: a long-standing historical debate solved through stable isotope analysis. Sci. Rep. 6, 36249 (2016).
CAS  PubMed  PubMed Central  Article  Google Scholar 

56.
Jackson, J. B. et al. Historical overfishing and the recent collapse of coastal ecosystems. Science 293, 629–637 (2001).
CAS  PubMed  Article  PubMed Central  Google Scholar 

57.
Brewington, S. et al. Islands of change vs. islands of disaster: managing pigs and birds in the Anthropocene of the North Atlantic. Holocene 25, 1676–1684 (2015).
Article  Google Scholar 

58.
Hicks, M. et al. in The Oxford Handbook of Historical Ecology and Applied Archaeology (eds Isendahl, C. & Stump, D.) Ch. 12 (Oxford Univ. Press, 2019).

59.
Grayson, D. K. & Delpech, F. Pleistocene reindeer and global warming. Conserv. Biol. 19, 557–562 (2005).
Google Scholar 

60.
Enghoff, I. B., MacKenzie, B. R. & Nielson, E. E. The Danish fish fauna during the warm Atlantic period (ca. 7000–3900 BC): forerunner of future changes? Fish. Res. 87, 167–180 (2007).
Article  Google Scholar 

61.
Tengberg, A. et al. Cultural ecosystem services provided by landscapes: assessment of heritage values and identity. Ecosyst. Serv. 2, 14–26 (2012).
Article  Google Scholar 

62.
Walter, R. K. & Hamilton, R. J. A cultural landscape approach to community-based conservation in Solomon Islands. Ecol. Soc. 19, 41 (2014).
Article  Google Scholar 

63.
Ekblom, A., Shoemaker, A., Gillson, L., Lane, P. & Lindholm, K. J. Conservation through biocultural heritage—examples from sub-Saharan Africa. Land 8, 5 (2019).
Article  Google Scholar 

64.
Bliege Bird, R., Bird, D. W., Codding, B. F., Parker, C. H. & Jones, J. H. The “fire stick farming” hypothesis: Australian Aboriginal foraging strategies, biodiversity, and anthropogenic fire mosaics. Proc. Natl Acad. Sci. USA 105, 14796–14801 (2008).
CAS  PubMed  Article  Google Scholar 

65.
Bowman, D. M. et al. Fire in the Earth system. Science 324, 481–484 (2009).
CAS  Article  Google Scholar 

66.
Bowman, D. M. et al. Pyrodiversity is the coupling of biodiversity and fire regimes in food webs. Philos. Trans. R. Soc. Lond. B 371, 20150169 (2016).
Article  Google Scholar 

67.
Kelly, L. T. & Brotons, L. Using fire to promote biodiversity. Science 355, 1264–1265 (2017).
CAS  PubMed  Article  Google Scholar 

68.
Beale, C. M. et al. Pyrodiversity interacts with rainfall to increase bird and mammal richness in African savannas. Ecol. Lett. 21, 557–567 (2018).
PubMed  PubMed Central  Article  Google Scholar 

69.
Gillson, L., Whitlock, C. & Humphrey, G. Resilience and fire management in the Anthropocene. Ecol. Soc. 24, 14 (2019).
Article  Google Scholar 

70.
Berna, F. et al. Microstratigraphic evidence of in situ fire in the Acheulean strata of Wonderwerk Cave, Northern Cape province, South Africa. Proc. Natl Acad. Sci. USA 109, E1215–E1220 (2012).
CAS  PubMed  Article  Google Scholar 

71.
Hlubik, S., Berna, F., Feibel, C., Braun, D. & Harris, J. W. K. Researching the nature of fire at 1.5 Mya on the site of FxJj20 AB, Koobi Fora, Kenya, using high-resolution spatial analysis and FTIR spectrometry. Curr. Anthropol. 58, S243–S257 (2017).
Article  Google Scholar 

72.
Yibarbuk, D. et al. Fire ecology and Aboriginal land management in central Arnhem Land, northern Australia: a tradition of ecosystem management. J. Biogeogr. 28, 325–343 (2001).
Article  Google Scholar 

73.
Black, B. A., Ruffner, C. M. & Abrams, M. D. Native American influences on the forest composition of the Allegheny Plateau, northwest Pennsylvania. Can. J. For. Res. 36, 1266–1275 (2006).
Article  Google Scholar 

74.
Marlon, J. R. et al. Climate and human influences on global biomass burning over the past two millennia. Nat. Geosci. 1, 697–702 (2008).
CAS  Article  Google Scholar 

75.
Bowman, D. M., O’Brien, J. A. & Goldammer, J. G. Pyrogeography and the global quest for sustainable fire management. Annu. Rev. Env. Res. 38, 57–80 (2013).
Article  Google Scholar 

76.
Trauernicht, C., Brook, B. W., Murphy, B. P., Williamson, G. J. & Bowman, D. M. J. S. Local and global pyrogeographic evidence that indigenous fire management creates pyrodiversity. Ecol. Evol. 5, 1908–1918 (2015).
PubMed  PubMed Central  Article  Google Scholar 

77.
Maezumi, S. Y. et al. New insights from pre-Columbian land use and fire management in Amazonian Dark Earth forests. Front. Ecol. Evol. 6, 111 (2018).
Article  Google Scholar 

78.
Bowman, D. M. et al. The human dimension of fire regimes on Earth. J. Biogeogr. 38, 2223–2236 (2011).
PubMed  PubMed Central  Article  Google Scholar 

79.
Nowacki, G. J. & Abrams, M. D. The demise of fire and “mesophication” of forests in the eastern United States. BioScience 58, 123–138 (2008).
Article  Google Scholar 

80.
Russell-Smith, J. et al. Managing fire regimes in north Australian savannas: applying Aboriginal approaches to contemporary global problems. Front. Ecol. Env. 11, e55–e63 (2013).
Google Scholar 

81.
Archibald, S. Managing the human component of fire regimes: lessons from Africa. Philos. Trans. R. Soc. Lond. B 371, 20150346 (2016).
Article  CAS  Google Scholar 

82.
Roos, C. I. et al. Living on a flammable planet: interdisciplinary, cross-scalar and varied cultural lessons, prospects and challenges. Philos. Trans. R. Soc. Lond. B 371, 20150469 (2016).
Article  Google Scholar 

83.
North, M. P. et al. Reform forest fire management. Science 349, 1280–1281 (2015).
CAS  PubMed  Article  Google Scholar 

84.
Lawes, M. J. et al. Small mammals decline with increasing fire extent in northern Australia: evidence from long-term monitoring in Kakadu National Park. Int. J. Wildland Fire 23, 712–722 (2015).
Article  Google Scholar 

85.
Edwards, A., Russell-Smith, J. & Meyer, M. Contemporary fire regime risks to key ecological assets and processes in north Australian savannas. Int. J. Wildland Fire 24, 857–870 (2015).
Article  Google Scholar 

86.
Bliege Bird, R., Codding, B. F., Kauhanen, P. G. & Bird, D. W. Aboriginal hunting buffers climate-driven fire-size variability in Australia’s spinifex grasslands. Proc. Natl Acad. Sci. USA 109, 10287–10292 (2012).
PubMed  Article  Google Scholar 

87.
Whitehead, P. J., Bowman, D. M., Preece, N., Fraser, F. & Cooke, P. Customary use of fire by indigenous peoples in northern Australia: its contemporary role in savanna management. Int. J. Wildland Fire 12, 415–425 (2003).
Article  Google Scholar 

88.
Mitchell, R. J. et al. Future climate and fire interactions in the southeastern region of the United States. For. Ecol. Manag. 327, 316–326 (2014).
Article  Google Scholar 

89.
Pechony, O. & Shindell, D. T. Driving forces of global wildfires over the past millennium and the forthcoming century. Proc. Natl. Acad. Sci. USA 107, 19167–19170 (2010).
CAS  PubMed  Article  Google Scholar 

90.
Whitehead, P. J., Purdon, P., Russell-Smith, J., Cooke, P. M. & Sutton, S. The management of climate change through prescribed savanna burning: emerging contributions of indigenous people in northern Australia. Public Admin. Dev. 28, 374–385 (2008).
Article  Google Scholar 

91.
Mistry, J., Bilbao, B. A. & Berardi, A. Community owned solutions for fire management in tropical ecosystems: case studies from Indigenous communities of South America. Philos. Trans. R. Soc. Lond. B 371, 20150174 (2016).
Article  CAS  Google Scholar 

92.
Gillson, L. & Willis, K. J. ‘As Earth’s testimonies tell’: wilderness conservation in a changing world. Ecol. Lett. 7, 990–998 (2004).
Article  Google Scholar 

93.
Vitousek, P. M., Ehrlich, P. R., Ehrlich, A. H. & Matson, P. A. Human appropriation of the products of photosynthesis. BioScience 36, 368–373 (1986).
Article  Google Scholar 

94.
Haberl, H. et al. Quantifying and mapping the human appropriation of net primary production in earth’s terrestrial ecosystems. Proc. Natl Acad. Sci. USA 104, 12942–12947 (2007).
CAS  PubMed  Article  Google Scholar 

95.
Khush, G. S. Green revolution: the way forward. Nat. Rev. Genet. 2, 815–822 (2001).
CAS  PubMed  Article  Google Scholar 

96.
Foley, J. A. et al. Solutions for a cultivated planet. Nature 478, 337–342 (2011).
CAS  PubMed  Article  Google Scholar 

97.
Tilman, D., Cassman, K. G., Matson, P. A., Naylor, R. & Polasky, S. Agricultural sustainability and intensive production practices. Nature 418, 671–677 (2002).
CAS  PubMed  Article  Google Scholar 

98.
Renard, D. et al. Ecological engineers ahead of their time: the functioning of pre-Columbian raised-field agriculture and its potential contributions to sustainability today. Ecol. Eng. 45, 30–44 (2012).
Article  Google Scholar 

99.
Kunen, J. L. Ancient Maya agricultural installations and the development of intensive agriculture in NW Belize. J. Field. Archaeol. 28, 325–346 (2001).
Article  Google Scholar 

100.
Erickson, C. L. in Managing Change: Sustainable Approaches to the Conservation of the Built Environment (eds Erickson, C. L. et al.) 181–204 (Getty Conservation Institute, 2003).

101.
Sandor, J. A. & Eash, N. S. Significance of ancient agricultural soils for long‐term agronomic studies and sustainable agriculture research. Agron. J. 83, 29–37 (1991).
Article  Google Scholar 

102.
Marston, J. M. Modeling resilience and sustainability in ancient agricultural systems. J. Ethnobiol. 35, 585–605 (2015).
Article  Google Scholar 

103.
Logan, A. L., Stump, D., Goldstein, S. T., Orijemie, E. A. & Schoeman, M. H. Usable pasts forum: critically engaging food security. Afr. Archaeol. Rev. 36, 419–438 (2019).
Article  Google Scholar 

104.
Stump, D. “Ancient and backward or long-lived and sustainable?” The role of the past in debates concerning rural livelihoods and resource conservation in eastern Africa. World Dev. 38, 1251–1122 (2010).
Article  Google Scholar 

105.
Spriggs, M. in The Oxford Handbook of Historical Ecology and Applied Archaeology (eds Isendahl, C. & Stump, D.) 395–411 (Oxford Univ. Press, 2019).

106.
Herath, S., Mishra, B., Wong, P. & Weerakoon, S. B. in Resilient Asia: Fusion of Traditional and Modern Systems for a Sustainable Future (eds Takeuchi, K. et al.) 151–187 (Springer, 2018).

107.
Lang, C. & Stump, D. Geoarchaeological evidence for the construction, irrigation, cultivation, and resilience of 15th–18th century AD terraced landscape at Engaruka, Tanzania. Quat. Res. 88, 382–399 (2017).
Article  Google Scholar 

108.
Abeywardana, N., Schütt, B., Wagalawatta, T. & Bebermeier, W. Indigenous agricultural systems in the Dry Zone of Sri Lanka: management transformation assessment and sustainability. Sustainability 11, 910 (2019).
Article  Google Scholar 

109.
Kendall, A. & Drew, D. in The Oxford Handbook of Historical Ecology and Applied Archaeology (eds Isendahl, C. & Stump, D.) 423–440 (Oxford Univ. Press, 2019).

110.
Erickson, C. L. & Candler, K. L. in Fragile Lands of Latin America: Strategies For Sustainable Development (ed. Browder, J. O.) 230–248 (Westview Press, 1989).

111.
Erickson, C. L. Raised field agriculture in the Lake Titicaca Basin: putting ancient agriculture back to work. Expedition 30, 8–16 (1988).
Google Scholar 

112.
McKey, D. et al. Pre-Columbian agricultural landscapes, ecosystem engineers, and self-organized patchiness in Amazonia. Proc. Natl Acad. Sci. USA 107, 7823–7828 (2010).
CAS  PubMed  Article  PubMed Central  Google Scholar 

113.
Lombardo, U., Canal-Beeby, E., Fehr, S. & Veit, H. Raised fields in the Bolivian Amazonia: a prehistoric green revolution or a flood risk mitigation strategy? J. Archaeol. Sci. 38, 502–512 (2011).
Article  Google Scholar 

114.
Kurashima, N., Fortini, L. & Ticktin, T. The potential of indigenous agricultural food production under climate change in Hawaiʻi. Nat. Sustain. 2, 191–199 (2019).
Article  Google Scholar 

115.
Marshall, K. et al. Restoring people and productivity to Puanui: challenges and opportunities in the restoration of an intensive rain-fed Hawaiian field system. Ecol. Soc. 22, 23 (2017).
Article  Google Scholar 

116.
Lincoln, N. K. et al. Restoration of ‘Āina Malo’o on Hawai’i Island: expanding biocultural relationships. Sustainability 10, 3985 (2018).
Article  Google Scholar 

117.
Atlas, W. I. et al. Ancient fish weir technology for modern stewardship: lessons from community-based salmon monitoring. Ecosyst. Health Sustain. 3, 1341284 (2017).
Article  Google Scholar 

118.
Rodrigues, L., Lombardo, U., Beeby, E. C. & Veit, H. Linking soil properties and pre-Columbian agricultural strategies in the Bolivian lowlands: the case of raised fields in Exaltación. Quat. Int. 437, 143–155 (2017).
Article  Google Scholar 

119.
Iriarte, J. et al. Fire-free land use in pre-1492 Amazonian savannas. Proc. Natl Acad. Sci. USA 109, 6473–6478 (2012).
CAS  PubMed  Article  PubMed Central  Google Scholar 

120.
Herrera, A. in The Oxford Handbook of Historical Ecology and Applied Archaeology (eds Isendahl, C. & Stump, D.) 459–479 (Oxford Univ. Press, 2019).

121.
Barthel, S. & Isendahl, C. Urban gardens, agriculture, and water management: sources of resilience for long-term food security in cities. Ecol. Econ. 86, 224–234 (2013).
Article  Google Scholar 

122.
Barthel, S., Crumley, C. & Svedin, U. Bio-cultural refugia: combating the erosion of diversity in landscapes of food production. Ecol. Soc. 18, 71 (2013).
Article  Google Scholar 

123.
Maezumi, S. The legacy of 4,500 years of polyculture agroforestry in the eastern Amazon. Nat. Plants 4, 540–547 (2018).
PubMed  PubMed Central  Article  Google Scholar 

124.
Barthel, S., Crumley, C. & Svedin, U. Bio-cultural refugia—safeguarding diversity of practices for food security and biodiversity. Glob. Environ. Change 23, 1142–1152 (2013).
Article  Google Scholar 

125.
Poschlod, P. & Braun-Reichert, R. Small natural features with large ecological roles in ancient agricultural landscapes of Central Europe-history, value, status, and conservation. Biol. Conserv. 211, 60–68 (2017).
Article  Google Scholar 

126.
Smýkal, P., Nelson, M. N., Berger, J. D. & Von Wettberg, E. J. The impact of genetic changes during crop domestication. Agronomy 8, 119 (2018).
Article  Google Scholar 

127.
Massawe, F., Mayes, S. & Cheng, A. Crop diversity: an unexploited treasure trove for food security. Trends Plant Sci. 21, 365–368 (2016).
CAS  PubMed  Article  PubMed Central  Google Scholar 

128.
Cheng, A. Shaping a sustainable food future by rediscovering long-forgotten ancient grains. Plant Sci. 269, 136–142 (2018).
CAS  PubMed  Article  PubMed Central  Google Scholar 

129.
Mueller, N. G., Fritz, G. J., Patton, P., Carmody, S. & Horton, E. T. Growing the lost crops of eastern North America’s original agricultural system. Nat. Plants 3, 17092 (2017).
PubMed  Article  PubMed Central  Google Scholar 

130.
Logan, A. L. “Why Can’t People Feed Themselves?”: archaeology as alternative archive of food security in Banda, Ghana. Am. Anthropol. 118, 508–524 (2016).
Article  Google Scholar 

131.
Mueller, N. G., White, A. & Szilagyi, P. Experimental cultivation of eastern North America’s lost crops: insights into agricultural practice and yield potential. J. Ethnobiol. 39, 549–566 (2019).
Article  Google Scholar 

132.
Palmer, S. A., Smith, O. & Allaby, R. G. The blossoming of plant archaeogenetics. Ann. Anat. 194, 146–156 (2012).
CAS  PubMed  Article  PubMed Central  Google Scholar 

133.
Østerberg, J. T. et al. Accelerating the domestication of new crops: feasibility and approaches. Trends Plant Sci. 22, 373–384 (2017).
PubMed  Article  CAS  PubMed Central  Google Scholar 

134.
McNeill, J. R. & Winiwarter, V. Breaking the sod: humankind, history, and soil. Science 304, 1627–1629 (2004).
CAS  PubMed  Article  PubMed Central  Google Scholar 

135.
Brown, A. G. & Walsh, K. Societal stability and environmental change: examining the archaeology‐soil erosion paradox. Geoarchaeology 32, 23–35 (2017).
Article  Google Scholar 

136.
Sandor, J. A. & Homburg, J. A. Anthropogenic soil change in ancient and traditional agricultural fields in arid to semiarid regions of the Americas. J. Ethnobiol. 37, 196–217 (2017).
Article  Google Scholar 

137.
Glaser, B., Haumaier, L., Guggenberger, G. & Zech, W. The ‘Terra Preta’ phenomenon: a model for sustainable agriculture in the humid tropics. Naturwissenschaften 88, 37–41 (2001).
CAS  PubMed  Article  PubMed Central  Google Scholar 

138.
Lehmann, J., Kern, D. C., Glaser, B. & Woods, W. I. (eds) Amazonian Dark Earths: Origin, Properties, Management (Springer, 2007).

139.
Blume, H. P. & Leinweber, P. Plaggen soils: landscape history, properties, and classification. J. Plant Nutr. Soil Sci. 16, 319–327 (2004).
Article  Google Scholar 

140.
Davidson, D. A., Dercon, G., Stewart, M. & Watson, F. The legacy of past urban waste disposal on local soils. J. Archaeol. Sci. 33, 778–783 (2006).
Article  Google Scholar 

141.
Sandor, J. A. & Eash, N. S. Ancient agricultural soils in the Andes of southern Peru. Soil Sci. Soc. Am. J. 59, 170–179 (1995).
CAS  Article  Google Scholar 

142.
Fairhead, J. & Leach, M. in Amazonian Dark Earths: Wim Sombroek’s Vision (eds Woods, W. I. et al.) 265–278 (Springer, 2009).

143.
McFadgen, B. G. Maori plaggen soils in New Zealand, their origin and properties. J. R. Soc. N. Z. 10, 3–18 (1980).
Article  Google Scholar 

144.
Calvelo Pereira, R. et al. Detailed carbon chemistry in charcoals from pre‐European Māori gardens of New Zealand as a tool for understanding biochar stability in soils. Eur. J. Soil Sci. 65, 83–95 (2014).
CAS  Article  Google Scholar 

145.
Downie, A. E., Van Zwieten, L., Smernik, R. J., Morris, S. & Munroe, P. R. Terra Preta Australis: reassessing the carbon storage capacity of temperate soils. Agric. Ecosyst. Environ. 140, 137–147 (2011).
Article  Google Scholar 

146.
Kern, J., Giani, L., Teixeira, W., Lanza, G. & Glaser, B. What can we learn from ancient fertile anthropic soil (Amazonian Dark Earths, shell mounds, Plaggen soil) for soil carbon sequestration? CATENA 172, 104–112 (2019).
CAS  Article  Google Scholar 

147.
Woolf, D., Amonette, J. E., Street-Perrott, F. A., Lehmann, J. & Joseph, S. Sustainable biochar to mitigate global climate change. Nat. Commun. 1, 56 (2010).
PubMed  Article  CAS  PubMed Central  Google Scholar 

148.
Bezerra, J., Turnhout, E., Rittl, T. F., Arts, B. & Kuyper, T. W. The promises of the Amazonian soil: shifts in discourses of Terra Preta and biochar. J Environ. Policy Plan. 21, 623–635 (2019).
Article  Google Scholar 

149.
Novotny, E. H. et al. Lessons from the Terra Preta de Índios of the Amazon region for the utilisation of charcoal for soil amendment. J. Braz. Chem. Soc. 20, 1003–1010 (2009).
CAS  Article  Google Scholar 

150.
Lehmann, J. & Joseph, S. in Biochar for Environmental Management (eds Lehmann, J. & Joseph, S.) 1–14 (Routledge, 2015).

151.
Kim, J. S., Sparovek, G., Longo, R. M., De Melo, W. J. & Crowley, D. Bacterial diversity of terra preta and pristine forest soil from the Western Amazon. Soil Biol. Biochem. 39, 684–690 (2007).
CAS  Article  Google Scholar 

152.
Glaser, B. & Birk, J. J. State of the scientific knowledge on properties and genesis of anthropogenic dark earths in Central Amazonia (terra preta de Índio). Geochim. Cosmochim. Acta 82, 39–51 (2012).
CAS  Article  Google Scholar 

153.
Jorio, A. et al. Microscopy and spectroscopy analysis of carbon nanostructures in highly fertile Amazonian anthrosoils. Soil Tillage Res. 122, 61–66 (2012).
Article  Google Scholar 

154.
More, A. F. et al. Next-generation ice core technology reveals true minimum natural levels of lead (Pb) in the atmosphere: insights from the Black Death. GeoHealth 1, 211–219 (2017).
PubMed  PubMed Central  Article  Google Scholar 

155.
Factura, H. et al. Terra Preta sanitation: re-discovered from an ancient Amazonian civilisation – integrating sanitation, bio-waste management and agriculture. Water Sci. Technol. 61, 2673–2679 (2010).
CAS  PubMed  Article  PubMed Central  Google Scholar 

156.
Glaser, B. Prehistorically modified soils of central Amazonia: a model for sustainable agriculture in the twenty-first century. Philos. Trans. R. Soc. Lond. B 362, 187–196 (2007).
CAS  Article  Google Scholar 

157.
Fedick, S. L. & Morrison, B. A. Ancient use and manipulation of landscape in the Yalahau region of the northern Maya lowlands. Agric. Hum. Values 21, 207–219 (2004).
Article  Google Scholar 

158.
Sedov, S. et al. Soil genesis in relation to landscape evolution and ancient sustainable land use in the northeastern Yucatan Peninsula, Mexico. Atti Soc. Tosc. Sci. Nat. Mem. A 112, 115–126 (2007).
Google Scholar 

159.
Acksel, A., Kapenberg, A., Kühn, P. & Leinweber, P. Human activity formed deep, dark topsoils around the Baltic Sea. Geoderma Region. 10, 93–101 (2017).
Article  Google Scholar 

160.
Marshall, F. et al. Ancient herders enriched and restructured African grasslands. Nature 561, 387–390 (2018).
CAS  PubMed  Article  PubMed Central  Google Scholar 

161.
Muchiru, A. N., Western, D. & Reid, R. S. The impact of abandoned pastoral settlements on plant and nutrient succession in an African savanna ecosystem. J. Arid Environ. 73, 322–331 (2009).
Article  Google Scholar 

162.
Bogaard, A. et al. Crop manuring and intensive land management by Europe’s first farmers. Proc. Natl Acad. Sci. USA 110, 12589–12594 (2013).
CAS  PubMed  Article  PubMed Central  Google Scholar 

163.
Beach, T., Luzzadder-Beach, S., Dunning, N., Hageman, J. & Lohse, J. Upland agriculture in the Maya Lowlands: ancient Maya soil conservation in northwestern Belize. Geogr. Rev. 92, 372–397 (2002).
Article  Google Scholar 

164.
Akimoto, H. Global air quality and pollution. Science 302, 1716–1719 (2003).
CAS  PubMed  Article  PubMed Central  Google Scholar 

165.
Hong, S., Candelone, J. P., Patterson, C. & Boutron, C. F. History of ancient copper smelting pollution during Roman and medieval times recorded in Greenland ice. Science 272, 246–249 (1996).
CAS  Article  Google Scholar 

166.
Hong, S., Candelone, J. P., Patterson, C. C. & Boutron, C. F. Greenland ice evidence of hemispheric lead pollution two millennia ago by Greek and Roman civilizations. Science 265, 1841–1843 (1994).
CAS  PubMed  Article  PubMed Central  Google Scholar 

167.
Shotyk, W. et al. History of atmospheric lead deposition since 12,370 14C yr BP from a peat bog, Jura Mountains, Switzerland. Science 281, 1635–1640 (1998).
CAS  PubMed  Article  PubMed Central  Google Scholar 

168.
Borsos, E., Makra, L., Béczi, R., Vitányi, B. & Szentpéteri, M. Anthropogenic air pollution in the ancient times. Acta Climatol. Chorolog. 36–37, 5–15 (2003).
Google Scholar 

169.
Pyatt, F. B. & Grattan, J. P. Some consequences of ancient mining activities on the health of ancient and modern human populations. J. Public Health 23, 235–236 (2001).
CAS  Article  Google Scholar 

170.
Pyatt, F. B., Pyatt, A. J., Walker, C., Sheen, T. & Grattan, J. P. The heavy metal content of skeletons from an ancient metalliferous polluted area in southern Jordan with particular reference to bioaccumulation and human health. Ecotoxicol. Environ. Saf. 60, 295–300 (2005).
CAS  PubMed  Article  PubMed Central  Google Scholar 

171.
Longman, J., Veres, D., Finsinger, W. & Ersek, V. Exceptionally high levels of lead pollution in the Balkans from the Early Bronze Age to the Industrial Revolution. Proc. Natl Acad. Sci. USA 115, E5661–E5668 (2018).
PubMed  Article  CAS  PubMed Central  Google Scholar 

172.
Renberg, I. et al. Environmental history: a piece in the puzzle for establishing plans for environmental management. J. Environ. Manag. 90, 2794–2800 (2009).
CAS  Article  Google Scholar 

173.
Bennion, H., Battarbee, R. W., Sayer, C. D., Simpson, G. L. & Davidson, T. A. Defining reference conditions and restoration targets for lake ecosystems using palaeolimnology: a synthesis. J. Paleolimnol. 45, 533–544 (2011).
Article  Google Scholar 

174.
Bindler, R., Rydberg, J. & Renberg, I. Establishing natural sediment reference conditions for metals and the legacy of long-range and local pollution on lakes in Europe. J. Paleolimnol. 45, 519–531 (2011).
Article  Google Scholar 

175.
Fuller, D. Q. et al. The contribution of rice agriculture and livestock pastoralism to prehistoric methane levels: an archaeological assessment. Holocene 21, 743–759 (2011).
Article  Google Scholar 

176.
Ruddiman, W. F. et al. Late Holocene climate: natural or anthropogenic? Rev. Geophys. 54, 93–118 (2016).
Article  Google Scholar 

177.
Ruddiman, W. F. The Anthropocene. Annu. Rev. Earth Planet. Sci. 41, 45–68 (2013).
CAS  Article  Google Scholar 

178.
Pyatt, F. B. Copper and lead bioaccumulation by Acacia retinoides and Eucalyptus torquata in sites contaminated as a consequence of extensive ancient mining activities in Cyprus. Ecotoxicol. Environ. Saf. 50, 60–64 (2001).
CAS  PubMed  Article  Google Scholar 

179.
Pyatt, F. B., Gilmore, G., Grattan, J. P., Hunt, C. O. & McLaren, S. An imperial legacy? An exploration of the environmental impact of ancient metal mining and smelting in southern Jordan. J. Archaeol. Sci. 27, 771–778 (2000).
Article  Google Scholar 

180.
Bindler, R., Renberg, I. & Klaminder, J. Bridging the gap between ancient metal pollution and contemporary biogeochemistry. J. Paleolimnol. 40, 755–770 (2008).
Article  Google Scholar 

181.
Farmer, J. G. et al. Historical accumulation rates of mercury in four Scottish ombrotrophic peat bogs over the past 2000 years. Sci. Total Environ. 407, 5578–5588 (2009).
CAS  PubMed  Article  Google Scholar 

182.
Knabb, K. A. et al. Environmental impacts of ancient copper mining and metallurgy: multi-proxy investigation of human-landscape dynamics in the Faynan valley, southern Jordan. J. Archaeol. Sci. 74, 85–101 (2016).
CAS  Article  Google Scholar 

183.
Grattan, J. P., Gilbertson, D. D. & Hunt, C. O. The local and global dimensions of metalliferous pollution derived from a reconstruction of an eight thousand year record of copper smelting and mining at a desert-mountain frontier in southern Jordan. J. Archaeol. Sci. 34, 83–110 (2007).
Article  Google Scholar 

184.
Wilson, B. & Pyatt, F. B. Heavy metal bioaccumulation by the important food plant, Olea europaea L., in an ancient metalliferous polluted area of Cyprus. Bull. Environ. Contam. Toxicol. 78, 390–394 (2007).
CAS  PubMed  Article  Google Scholar 

185.
Seto, K. C. & Shepherd, J. M. Global urban land-use trends and climate impacts. Curr. Opin. Environ. Sustain. 1, 89–95 (2009).
Article  Google Scholar 

186.
Simon, D. & Adam-Bradford, A. in Balanced Urban Development: Options and Strategies for Liveable Cities (eds Maheshwari, B. et al.) 57–83 (Springer, 2016).

187.
Isendahl, C. & Smith, M. E. Sustainable agrarian urbanism: the low-density cities of the Mayas and Aztecs. Cities 31, 132–143 (2013).
Article  Google Scholar 

188.
Lucero, L. J., Fletcher, R. & Coningham, R. From ‘collapse’ to urban diaspora: the transformation of low-density, dispersed agrarian urbanism. Antiquity 89, 1139–1154 (2015).
Article  Google Scholar 

189.
Fletcher, R. in The Comparative Archaeology of Complex Societies (ed. Smith, M. E.) 285–320 (Cambridge Univ. Press, 2011).

190.
Heckenberger, M. J. et al. Pre-Columbian urbanism, anthropogenic landscapes, and the future of the Amazon. Science 321, 1214–1217 (2008).
CAS  PubMed  Article  Google Scholar 

191.
Barthel, S. et al. Global urbanization and food production in direct competition for land: leverage places to mitigate impacts on SDG2 and on the Earth System. Anthropocene Rev. 6, 71–97 (2019).
Article  Google Scholar 

192.
Wilkinson, A. The Garden in Ancient Egypt (Rubicon Press, 1998).

193.
Edmondson, J. L. et al. The hidden potental of urban horticulture. Nat. Food 1, 155–159 (2020).
Article  Google Scholar 

194.
Scarborough, V. L. et al. Water and sustainable land use at the ancient tropical city of Tikal, Guatemala. Proc. Natl Acad. Sci. USA 109, 12408–12413 (2012).
CAS  PubMed  Article  Google Scholar 

195.
Angelakis, A. N. & Spyridakis, S. V. Major urban water and wastewater systems in Minoan Crete, Greece. Water Sci. Technol. Water Supply 13, 564–573 (2013).
Article  Google Scholar 

196.
Mays, L., Antoniou, G. P. & Angelakis, A. N. History of water cisterns: legacies and lesson. Water 5, 1916–1940 (2013).
Article  Google Scholar 

197.
French, K. D. & Duffy, C. J. Understanding ancient Maya water resources and the implications for a more sustainable future. Wiley Interdiscip. Rev. Water 1, 305–313 (2014).
Article  Google Scholar 

198.
Chase, A. S. Beyond elite control: residential reservoirs at Caracol, Belize. Wiley Interdiscip. Rev. Water 3, 885–897 (2016).
Article  Google Scholar 

199.
Rosenzweig, C. et al. Attributing physical and biological impacts to anthropogenic climate change. Nature 453, 353–357 (2008).
CAS  PubMed  Article  Google Scholar 

200.
Van de Noort, R. Conceptualising climate change archaeology. Antiquity 85, 1039–1048 (2011).
Article  Google Scholar 

201.
Hudson, M. J., Aoyama, M., Hoover, K. C. & Uchiyama, J. Prospects and challenges for an archaeology of global climate change. Wiley Interdiscip. Rev. Clim. Change 3, 313–328 (2012).
Article  Google Scholar 

202.
Sandweiss, D. H. & Kelley, A. R. Archaeological contributions to climate change research: the archaeological record as a paleoclimatic and paleoenvironmental archive. Annu. Rev. Anthropol. 41, 371–391 (2012).
Article  Google Scholar 

203.
Rockman, M. & Hritz, C. Expanding use of archaeology in climate change response by changing its social environment. Proc. Natl Acad. Sci. USA 117, 8295–8302 (2020).
CAS  PubMed  Article  PubMed Central  Google Scholar 

204.
Douglass, K. & Cooper, J. Archaeology, environmental justice, and climate change on islands of the Caribbean and southwestern Indian Ocean. Proc. Natl Acad. Sci. USA 117, 8254–8262 (2020).
CAS  PubMed  Article  PubMed Central  Google Scholar 

205.
Nelson, M. C. et al. Climate challenges, vulnerabilities, and food security. Proc. Natl Acad. Sci. USA 113, 298–303 (2016).
CAS  PubMed  Article  PubMed Central  Google Scholar 

206.
Mitchell, P. Practising archaeology at a time of climatic catastrophe. Antiquity 82, 1093–1103 (2008).
Article  Google Scholar 

207.
Weiss, H. & Bradley, R. S. What drives societal collapse? Science 291, 609–610 (2001).
CAS  PubMed  Article  PubMed Central  Google Scholar 

208.
Haug, G. H. et al. Climate and the collapse of Maya civilization. Science 299, 1731–1735 (2003).
CAS  PubMed  Article  PubMed Central  Google Scholar 

209.
Weninger, B. et al. The impact of rapid climate change on prehistoric societies during the Holocene in the eastern Mediterranean. Doc. Praehistorica 36, 7–59 (2009).
Article  Google Scholar 

210.
Kennett, D. J. et al. Development and disintegration of Maya political systems in response to climate change. Science 338, 788–791 (2012).
CAS  PubMed  Article  PubMed Central  Google Scholar 

211.
Anderson, D. G., Maasch, K. A., Sandweiss, D. H. & Mayewski, P. A. in Climate Change and Cultural Dynamics: A Global Perspective on Mid-Holocene Transitions (eds Anderson, D. G. et al.) 1–23 (Academic Press, 2007).

212.
Kintigh, K. W. & Ingram, S. E. Was the drought really responsible? Assessing statistical relationships between climate extremes and cultural transitions. J. Archaeol. Sci. 89, 25–31 (2018).
Article  Google Scholar 

213.
Amand, F. S. et al. Leveraging legacy archaeological collections as proxies for climate and environmental research. Proc. Natl Acad. Sci. USA 117, 8287–8294 (2020).
Article  CAS  Google Scholar 

214.
Jones, T. L. et al. Environmental imperatives reconsidered: demographic crises in western North America during the Medieval climatic anomaly. Curr. Anthropol. 40, 137–170 (1999).
CAS  PubMed  Article  PubMed Central  Google Scholar 

215.
Mann, M. E. in Encyclopedia of Global Environmental Change (ed. MacCracken, M. C.) 504–509 (John Wiley & Sons, Ltd, 2002).

216.
Flohr, P., Fleitmann, D., Matthews, R., Matthews, W. & Black, S. Evidence of resilience to past climate change in Southwest Asia: early farming communities and the 9.2 and 8.2 ka events. Quat. Sci. Rev. 136, 23–39 (2016).
Article  Google Scholar 

217.
Buckley, B. M. et al. Climate as a contributing factor in the demise of Angkor, Cambodia. Proc. Natl Acad. Sci. USA 107, 6748–6752 (2010).
CAS  PubMed  Article  PubMed Central  Google Scholar 

218.
Roscoe, P. A changing climate for anthropological and archaeological research? Improving the climate‐change models. Am. Anthropol. 116, 535–548 (2014).
Google Scholar 

219.
Büntgen, U. et al. 2500 years of European climate variability and human susceptibility. Science 331, 578–582 (2011).
PubMed  Article  CAS  PubMed Central  Google Scholar 

220.
Petraglia, M. D., Groucutt, H., Guagnin, M., Breeze, P. S. & Boivin, N. Human responses to climate and ecosystem change in ancient Arabia. Proc. Natl Acad. Sci. USA 117, 8263–8270 (2020).
CAS  PubMed  Article  PubMed Central  Google Scholar 

221.
Manuel, M., Lightfoot, D. & Fattahi, M. The sustainability of ancient water control techniques in Iran: an overview. Water Hist. 10, 13–30 (2018).
Article  Google Scholar 

222.
Avriel-Avni, N., Avni, Y., Babad, A. & Meroz, A. Wisdom dwells in places: what can modern farmers learn from ancient agricultural systems in the desert of the Southern Levant? J. Arid Environ. 163, 86–98 (2019).
Article  Google Scholar 

223.
Lasaponara, R., Rojas, J. L. & Masini, N. in The Ancient Nasca World (eds Lasaponara, R. et al.) 279–327 (Springer, 2016).

224.
Bebermeier, W., Meister, J., Withanachchi, C. R., Middelhaufe, I. & Schütt, B. Tank cascade systems as a sustainable measure of watershed management in South Asia. Water 9, 231 (2017).
Article  Google Scholar 

225.
Altschul, J. H. et al. Opinion: Fostering synthesis in archaeology to advance science and benefit society. Proc. Natl Acad. Sci. USA 114, 10999–11002 (2017).
CAS  PubMed  Article  PubMed Central  Google Scholar 

226.
Tainter, J. The Collapse of Complex Societies (Cambridge Univ. Press, 1988).

227.
Redman, C. L. Human Impact on Ancient Environments (Univ. Arizona, 1999).

228.
Redman, C. L. Resilience theory in archaeology. Am. Anthropol. 107, 70–77 (2005).
Article  Google Scholar 

229.
Jenny, J.-P. et al. Human and climate global-scale imprint on sediment transfer during the Holocene. Proc. Natl Acad. Sci. USA 116, 22972–22976 (2019).
CAS  PubMed  Article  PubMed Central  Google Scholar 

230.
Kaplan, J. O., Krumhardt, K. M. & Zimmermann, N. The prehistoric and preindustrial deforestation of Europe. Quat. Sci. Rev. 28, 3016–3034 (2009).
Article  Google Scholar 

231.
Lane, P. Archaeology in the age of the Anthropocene: a critical assessment of its scope and societal contributions. J. Field Archaeol. 40, 485–498 (2015).
Article  Google Scholar 

232.
Catlin, K. A. Archaeology for the Anthropocene: scale, soil, and the settlement of Iceland. Anthropocene 15, 13–21 (2016).
Article  Google Scholar 

233.
Kintigh, K. W. et al. Grand challenges for archaeology. Proc. Natl Acad. Sci. USA 111, 879–880 (2014).
CAS  PubMed  Article  PubMed Central  Google Scholar 

234.
Smith, M. E. Sprawl, squatters and sustainable cities: can archaeological data shed light on modern urban issues? Camb. Archaeol. J. 20, 229–253 (2010).
Article  Google Scholar 

235.
Dave, R. Archaeology must open up to become more diverse. The Guardian (23 May 2016); https://go.nature.com/36mbRRl

236.
White, W. & Draycott, C. Why the whiteness of archaeology is a problem. Sapiens (7 July 2020); https://go.nature.com/3lhgS3T

237.
Smith, C. & Wobst, H. M. Indigenous Archaeologies: Decolonising Theory and Practice (Routledge, 2004).

238.
Hamilakis, Y. Decolonial archaeology as social justice. Antiquity 92, 518–520 (2018).
Article  Google Scholar 

239.
Mustaphi, C. J. C. et al. Integrating evidence of land use and land cover change for land management policy formulation along the Kenya-Tanzania borderlands. Anthropocene 28, 100228 (2019).
Article  Google Scholar 

240.
Widgren, M. in Rethinking Environmental History World-System History and Global Environmental Change (eds Hornberg, A. et al.) 61–77 (Rowman Altamira, 2007).

241.
Matthews, D. German humanities scholars’ unusual role. Inside Higher Ed (24 April 2020); https://go.nature.com/3nbVCNi

242.
Agnoletti, M. (ed.) The Conservation of Cultural Landscapes (CABI, 2006).

243.
Lowenthal, D. The Past is a Foreign Country – Revisited (Cambridge Univ. Press, 2015). More

Affiliations

Department of Biology, McGill University, Montreal, Quebec, Canada
Brian Leung & Anna L. Hargreaves

Bieler School of Environment, McGill University, Montreal, Quebec, Canada
Brian Leung

Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
Dan A. Greenberg

School of Biology and Ecology, University of Maine, Orono, ME, USA
Brian McGill

Mitchell Center for Sustainability Solutions, University of Maine, Orono, ME, USA
Brian McGill

Centre for Biological Diversity, University of St Andrews, St Andrews, UK
Maria Dornelas

Indicators and Assessments Unit, Institute of Zoology, Zoological Society of London, London, UK
Robin Freeman

Authors
Brian Leung

Anna L. Hargreaves

Dan A. Greenberg

Brian McGill

Maria Dornelas

Robin Freeman

Corresponding author
Correspondence to Brian Leung. More