Philippa Kaur

All methods were performed in accordance with the relevant guidelines and regulations.Study siteThe laboratory experiments on regeneration and wash resistance were conducted at the KCMUCo-PAMVERC Insecticide Testing Facility; while experimental hut study was carried out at Harusini, the facility’s field site located at Mabogini village (S03˚22.764’ E03˚720.793’), adjacent to Lower Moshi rice irrigation scheme in north-eastern Tanzania. The dominant vector at this site is An. arabiensis with moderate level of resistance to pyrethroids conferred by both oxidase and esterase activities32. In this study, pyrethroid-resistant laboratory reared An. gambiae Muleba-Kis mosquitoes were released into the huts for the release-recapture experiment.Test systemsNon-blood fed, 2–5 day old females of susceptible An. gambiae s.s. Kisumu strain and pyrethroid resistant An. gambiae s.s Muleba-Kis strain were used for the evaluation of efficacy in the laboratory (phase I). The Muleba-Kis strain has been colonized for more than 8 years and it is resistant to permethrin with fixed L1014S kdr frequency and metabolic resistance through increased oxidase activity has also been reported21. Only An. gambiae s.s Muleba-Kis were used in release-recapture experiments. The Kisumu strain is fully susceptible to insecticides and free of any detectable insecticide resistance mechanisms. The strain originated from Kisumu, Kenya and has been colonized for many years in laboratory. At the KCMUCo-PAMVERC Moshi insectary, the adult Kisumu strain mosquitoes are reared at a temperature of 24–27 °C, 75 ± 10% relative humidity (RH) and maintained under a dark:light regime of 12:12 h. The Muleba-Kis mosquitoes used for the release-recapture experiments were reared in the field insectary under ambient temperature and relative humidity and treated as previously explained21. The susceptibility status of these colonies is checked every three months using WHO susceptibility test33 and, CDC bottle bioassay test34. The colonies are regularly genotyped for kdr mutations using TaqMan assays35. To maintain the resistance of Muleba-Kis, larvae are frequently selected with alpha-cypermethrin.Regeneration timeTo determine the regeneration time of the insecticide-treated blankets, blankets were cut into 25 × 25 cm pieces and tested before washing and then washed and dried three times consecutively following WHO recommended procedures for LLINs36. The pieces were then re-tested after one, two, three, six and seven days post-washing using WHO cylinders against susceptible An. gambiae s.s (Kisumu).Graphs for 24-h mortality and 60 min knock down (KD) correlating to insecticide bioavailability, as measured by 3 min exposure in cylinder bioassays, were established before and after washing blanket pieces three times consecutively in a day, and tested within a maximum of seven days post-washing. The time in days required to reach initial mortality or 60 min KD plateau is the period required for full regeneration of insecticide-treated blanket.Wash resistanceWHO cylinder bioassays36 were used to assess the wash resistance for the blanket pieces washed 0, 5, 10, 15 and 20 times at the intervals equivalent to the regeneration time. Four pieces cut from 4 permethrin and 4 untreated blankets were used as positive and negative control respectively, against 4 pieces cut from 4 PBO–permethrin blankets.Bioassay proceduresFive, non-blood fed, 2–5 day old An. gambiae Kisumu or An. gambiae Muleba-Kis mosquitoes were exposed for 3 min or 30 min to blanket pieces in WHO cylinder. Bioassays were carried out at 27 ± 2 °C and 75 ± 10% RH. Knock-down was scored after 60 min post-exposure and mortality after 24 h. Fifty mosquitoes (5 mosquitoes per cylinder) were used on each 25 × 25 cm piece of blanket sample. After exposure, the mosquitoes were held for 24 h with access to 10% glucose solution in the paper cups covered with a net material. Mosquitoes exposed to untreated blanket were referred as a negative control.WHO tunnel test methodBlanket pieces which recorded ≤ 80% mortality in cylinder bioassay were tested in the tunnel assay using WHO guidelines. The tunnel was made of an acrylic square cylinder (25 cm in height, 25 cm in width, and 60 cm in length) divided into two sections using a blanket-covered frame fitted into a slot across the tunnel. During the assays a guinea pig was held in a small wooden cage (as a bait) in one of the sections and 50, non-blood fed, female An. gambiae Kisumu or An. gambiae Muleba-Kis aged 5–8 days were released in the other section at dusk and left overnight (13 h) for experimentation at 27 ± 2 °C and 75 ± 10% RH. The blanket surface was deliberately holed (nine 1-cm holes) to allow mosquitoes to contact the blanket material and penetrate to the baited chamber. Treated blankets were tested concurrently together with an untreated blanket. Scoring for the numbers of mosquitoes found alive or dead, fed or unfed, in each section were done in the morning. Mosquitoes found alive were removed and held in paper cups with labels corresponding to each tunnel sections under controlled conditions (25–27 °C and 75–85% RH) and fed on 10% glucose solution to monitor for delayed mortality post exposurely. Outcomes recorded were: mosquito penetration, blood feeding and mortality.Washing of blankets and whole nets for hut trialBlankets and whole nets were separately washed following WHOPES guidelines. In brief, each blanket/net was washed in Savon de Marseilles soap solution (2 g/L) for 10 min: 3 min stirring, 4 min soaking, then another 3 min stirring. This was followed by 2 rinse cycles of the same duration with water only. The water pH was 6 for all washes. The mean water hardness was within the WHOPES limit of ≤ 89 ppm. All nets used in the experimental hut study were cut with holes (4 cm × 4 cm) to simulate the conditions of a torn net. While nets were washed 20 times as per guidelines, blankets were only washed 10 times. To simulate a situation in emergence situations where washing is less frequent due to water scarcity30,31.Experimental hut trial:experimental hut designExperimental hut study was done in Lower Moshi using typical East African experimental huts design as described in the WHOPES35. Huts were constructed with brick walls and featured with cement plaster on the inside and a ceiling board, a metal iron sheet roof, open eaves with window and veranda traps on each side and window traps. Slight modifications from the original structure were made by installing metal eave baffles on two sides. The baffles allow mosquito entry but prevent exits. The window traps were used to collect mosquitoes that tend to exit the huts.Test item labelling, washing and perforatingBoth blankets and LLINs for the trial were distinctively labelled with fabric labels that withstand washes. For wash resistance, the blankets and nets were separately washed according to a protocol adapted from the standard WHO washing procedure36 at the interval equivalent to the regeneration time established in the laboratory for blanket and LLIN respectively. Before testing in the experimental huts, all nets were deliberately holed i.e. 30 holes measuring 4 × 4 cm were made in each net, 9 holes in each of the long side panels, and 6 holes at each short side (head- and foot-side panels) to enhance blood-feeding on the control arm.Test items packagingEach blanket and net were sealed in a plastic bag and then packed in the large plastic container. Each container was labelled for a single treatment to avoid cross contamination between test items.Experimental hut decontaminationA cone assay with 10 susceptible mosquitoes was performed on one wall per hut to rule out any contamination of the wall surface. Only huts with 24 h mortality of susceptible mosquitoes  More

Moberg, F. & Folke, C. Ecological goods and services of coral reef ecosystems. Ecol. Econ. 29, 215–233 (1999).Article 

Google Scholar 
Woodhead, A. J., Hicks, C. C., Norström, A. V., Williams, G. J. & Graham, N. A. J. Coral reef ecosystem services in the Anthropocene. Funct. Ecol. 33, 1023–1034 (2019).
Google Scholar 
Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82 (2017).Article 
ADS 
CAS 

Google Scholar 
Hughes, T. P., Kerry, J. T. & Simpson, T. Large-scale bleaching of corals on the Great Barrier Reef. Ecology 99, 501 (2017).Article 

Google Scholar 
Anthony, K. R. N., Kline, D. I., Diaz-Pulido, G., Dove, S. & Hoegh-Guldberg, O. Ocean acidification causes bleaching and productivity loss in coral reef builders. PNAS 105, 17442–17446 (2008).Article 
ADS 
CAS 

Google Scholar 
Courtial, L., Roberty, S., Shick, J. M., Houlbrèque, F. & Ferrier-Pagès, C. Interactive effects of ultraviolet radiation and thermal stress on two reef-building corals. Limnol. Oceanogr. 62, 1000–1013 (2017).Article 
ADS 

Google Scholar 
Jessen, C. et al. In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the Red Sea Coral Acropora hemprichii. PLoS ONE 8, e62091 (2013).Article 
ADS 
CAS 

Google Scholar 
Jessen, C., Roder, C., Villa Lizcano, J. F., Voolstra, C. R. & Wild, C. In-situ effects of simulated overfishing and eutrophication on benthic coral reef algae growth, succession, and composition in the Central Red Sea. PLoS ONE 8, e66992 (2013).Article 
ADS 
CAS 

Google Scholar 
Fabricius, K. E. Effects of terrestrial runoff on the ecology of corals and coral reefs: Review and synthesis. Mar. Pollut. Bull. 50, 125–146 (2005).Article 
CAS 

Google Scholar 
Hughes, T. P. et al. Climate change, human impacts, and the resilience of coral reefs. Science 301, 929–933 (2003).Article 
ADS 
CAS 

Google Scholar 
Fabricius, K. E., Cséke, S., Humphrey, C. & De’ath, G. Does trophic status enhance or reduce the thermal tolerance of scleractinian corals? A review, experiment and conceptual framework. PLoS ONE 8, e54399 (2013).Article 
ADS 
CAS 

Google Scholar 
McLachlan, R. H., Price, J. T., Solomon, S. L. & Grottoli, A. G. Thirty years of coral heat-stress experiments: A review of methods. Coral Reefs 39, 885–902 (2020).Article 

Google Scholar 
Fabricius, K. E. Factors determining the resilience of coral reefs to eutrophication: A review and conceptual model. In Coral Reefs: An Ecosystem in Transition (eds Dubinsky, Z. & Stambler, N.) (Springer, 2011).
Google Scholar 
Tilstra, A. et al. Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata. PeerJ. https://doi.org/10.7717/PEERJ.3802/ (2017).Article 

Google Scholar 
Connolly, S. R., Lopez-Yglesias, M. A. & Anthony, K. R. N. Food availability promotes rapid recovery from thermal stress in a scleractinian coral. Coral Reefs 31, 951–960 (2012).Article 
ADS 

Google Scholar 
Coles, S. L. & Brown, B. E. Coral bleaching—Capacity for acclimatization and adaptation. Adv. Mar. Biol. 46, 183 (2003).Article 
CAS 

Google Scholar 
Rosenberg, E., Koren, O., Reshef, L., Efrony, R. & Zilber-Rosenberg, I. The role of microorganisms in coral health, disease and evolution. Nat. Rev. Microbiol. 5, 355–362 (2007).Article 
CAS 

Google Scholar 
Szmant, A. M. Nutrient enrichment on coral reefs: Is it a major cause of coral reef decline? Estuaries 25, 743–766 (2002).Article 
CAS 

Google Scholar 
Atkinson, M. J., Carlson, B. & Crow, G. L. Coral growth in high-nutrient, low-pH seawater: A case study of corals cultured at the Waikiki Aquarium, Honolulu, Hawaii. Coral Reefs 14, 215–223 (1995).Article 
ADS 

Google Scholar 
Bongiorni, L., Shafir, S., Angel, D. & Rinkevich, B. Survival, growth and gonad development of two hermatypic corals subjected to in situ fish-farm nutrient enrichment. Mar. Ecol. Prog. Ser. 253, 137–144 (2003).Article 
ADS 

Google Scholar 
Grigg, R. W. Coral reefs in an urban embayment in Hawaii: A complex case history controlled by natural and anthropogenic stress. Coral Reefs 14, 253–266 (1995).Article 
ADS 

Google Scholar 
Fabricius, K. E. & De’ath, G. Identifying ecological change and its causes: A case study on coral reefs. Ecol. Appl. 14, 1448–1465 (2004).Article 

Google Scholar 
Ferrier-Pagès, C., Gattuso, J. P., Dallot, S. & Jaubert, J. Effect of nutrient enrichment on growth and photosynthesis of the zooxanthellate coral Stylophora pistillata. Coral Reefs 19, 103–113 (2000).Article 

Google Scholar 
Rosset, S., Wiedenmann, J., Reed, A. J. & D’Angelo, C. Phosphate deficiency promotes coral bleaching and is reflected by the ultrastructure of symbiotic dinoflagellates. Mar. Pollut. Bull. 118, 180–187 (2017).Article 
CAS 

Google Scholar 
Ban, S. S., Graham, N. A. J. & Connolly, S. R. Evidence for multiple stressor interactions and effects on coral reefs. Glob. Change Biol. 20, 681–697 (2014).Article 
ADS 

Google Scholar 
Wiedenmann, J. et al. Nutrient enrichment can increase the susceptibility of reef corals to bleaching. Nat. Clim. Change 3, 160–164 (2012).Article 
ADS 

Google Scholar 
Rädecker, N. et al. Heat stress destabilizes symbiotic nutrient cycling in corals. PNAS. https://doi.org/10.1073/pnas.2022653118 (2021).Article 

Google Scholar 
LaJeunesse, T. C. et al. Systematic revision of symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580 (2018).Article 
CAS 

Google Scholar 
Falkowski, P. G., Dubinsky, Z., Muscatine, L. & McCloskey, L. Population control in symbiotic corals—Ammonium ions and organic materials maintain the density of zooxanthellae. Bioscience 43, 606–611 (1993).Article 

Google Scholar 
Muscatine, L. & Pool, R. R. Regulation of numbers of intracellular algae. Proc. R. Soc. Lond. Ser. B Biol. Sci. 204, 131–139 (1979).ADS 
CAS 

Google Scholar 
Muller-Parker, G., D’Elia, C. F. & Cook, C. B. Interactions between corals and their symbiotic algae. Coral Reefs Anthr. https://doi.org/10.1007/978-94-017-7249-5_5 (2015).Article 

Google Scholar 
Rädecker, N., Pogoreutz, C., Voolstra, C. R., Wiedenmann, J. & Wild, C. Nitrogen cycling in corals: The key to understanding holobiont functioning? Trends Microbiol. 23, 490–497 (2015).Article 

Google Scholar 
Steinberg, R. K., Dafforn, K. A., Ainsworth, T. & Johnston, E. L. Know thy anemone: A review of threats to octocorals and anemones and opportunities for their restoration. Front. Mar. Sci. 7, 590 (2020).Article 

Google Scholar 
Inoue, S., Kayanne, H., Yamamoto, S. & Kurihara, H. Spatial community shift from hard to soft corals in acidified water. Nat. Clim. Change 3, 683–687 (2013).Article 
ADS 
CAS 

Google Scholar 
Wild, C. & Naumann, M. S. Effect of active water movement on energy and nutrient acquisition in coral reef-associated benthic organisms. PNAS 110, 8767–8768 (2013).Article 
ADS 
CAS 

Google Scholar 
Fox, H. E., Pet, J. S., Dahuri, R. & Caldwell, R. L. Recovery in rubble fields: Long-term impacts of blast fishing. Mar. Pollut. Bull. 46, 1024–1031 (2003).Article 
CAS 

Google Scholar 
Benayahu, Y. & Loya, Y. Settlement and recruitment of a soft coral: Why is Xenia macrospiculata a successful colonizer? Bull. Mar. Sci. 36, 177–188 (1985).
Google Scholar 
Norström, A. V., Nyström, M., Lokrantz, J. & Folke, C. Alternative states on coral reefs: Beyond coral-macroalgal phase shifts. Mar. Ecol. Prog. Ser. 376, 293–306 (2009).Article 
ADS 

Google Scholar 
Reverter, M., Helber, S. B., Rohde, S., De Goeij, J. M. & Schupp, P. J. Coral reef benthic community changes in the Anthropocene: Biogeographic heterogeneity, overlooked configurations, and methodology. Glob. Change Biol. 28, 1956–1971 (2022).Article 

Google Scholar 
Karcher, D. B. et al. Nitrogen eutrophication particularly promotes turf algae in coral reefs of the central Red Sea. PeerJ 2020, 1–25 (2020).
Google Scholar 
El-Khaled, Y. C. et al. Nitrogen fixation and denitrification activity differ between coral- and algae-dominated Red Sea reefs. Sci. Rep. 11, 1–15 (2021).Article 

Google Scholar 
Ruiz-Allais, J. P., Benayahu, Y. & Lasso-Alcalá, O. M. The invasive octocoral Unomia stolonifera (Alcyonacea, Xeniidae) is dominating the benthos in the Southeastern Caribbean Sea. Mem. la Fund La Salle Ciencias Nat. 79, 63–80 (2021).
Google Scholar 
Ruiz Allais, J. P., Amaro, M. E., McFadden, C. S., Halász, A. & Benayahu, Y. The first incidence of an alien soft coral of the family Xeniidae in the Caribbean, an invasion in eastern Venezuelan coral communities. Coral Reefs 33, 287 (2014).Article 
ADS 

Google Scholar 
Baum, G., Januar, I., Ferse, S. C. A., Wild, C. & Kunzmann, A. Abundance and physiology of dominant soft corals linked to water quality in Jakarta Bay, Indonesia. PeerJ 2016, 1–29 (2016).
Google Scholar 
Menezes, N. M. et al. New non-native ornamental octocorals threatening a South-west Atlantic reef. J. Mar. Biol. Assoc. U.K. https://doi.org/10.1017/S0025315421000849 (2022).Article 

Google Scholar 
Mantelatto, M. C., da Silva, A. G., dos Louzada, T. S., McFadden, C. S. & Creed, J. C. Invasion of aquarium origin soft corals on a tropical rocky reef in the southwest Atlantic. Brazil. Mar. Pollut. Bull. 130, 84–94 (2018).Article 
CAS 

Google Scholar 
Simancas-Giraldo, S. M. et al. Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication. PeerJ 9, e11663 (2021).Article 

Google Scholar 
Vollstedt, S., Xiang, N., Simancas-Giraldo, S. M. & Wild, C. Organic eutrophication increases resistance of the pulsating soft coral Xenia umbellata to warming. PeerJ 2020, 1–16 (2020).
Google Scholar 
Thobor, B. et al. The pulsating soft coral Xenia umbellata shows high resistance to warming when nitrate concentrations are low. Sci. Rep. https://doi.org/10.1038/s41598-022-21110-w (2022).Article 

Google Scholar 
Costa, O. S., Leão, Z. M. A. N., Nimmo, M. & Attrill, M. J. Nutrification impacts on coral reefs from northern Bahia, Brazil. Hydrobiologia 440, 307–315 (2000).Article 
CAS 

Google Scholar 
Fleury, B. G., Coll, J. C., Tentori, E., Duquesne, S. & Figueiredo, L. Effect of nutrient enrichment on the complementary (secondary) metabolite composition of the soft coral Sarcophyton ebrenbergi (Cnidaria: Octocorallia: Alcyonaceae) of the Great Barrier Reef. Mar. Biol. 136, 63–68 (2000).Article 
CAS 

Google Scholar 
Bednarz, V. N., Naumann, M. S., Niggl, W. & Wild, C. Inorganic nutrient availability affects organic matter fluxes and metabolic activity in the soft coral genus Xenia. J. Exp. Biol. 215, 3672–3679 (2012).CAS 

Google Scholar 
Bruno, J. F., Petes, L. E., Harvell, C. D. & Hettinger, A. Nutrient enrichment can increase the severity of coral diseases. Ecol. Lett. 6, 1056–1061 (2003).Article 

Google Scholar 
Ezzat, L., Maguer, J.-F.F., Grover, R. & Ferrier-Pagès, C. Limited phosphorus availability is the Achilles heel of tropical reef corals in a warming ocean. Sci. Rep. 6, 1–11 (2016).Article 

Google Scholar 
Tanaka, Y., Grottoli, A. G., Matsui, Y., Suzuki, A. & Sakai, K. Effects of nitrate and phosphate availability on the tissues and carbonate skeleton of scleractinian corals. Mar. Ecol. Prog. Ser. 570, 101–112 (2017).Article 
ADS 
CAS 

Google Scholar 
Liu, G., Strong, A. E., Skirving, W. & Arzayus, L. F. Overview of NOAA coral reef watch program’s near-real time satellite global coral bleaching monitoring activities. In Proc. 10th International Coral Reef Symposium, 1783–1793 (2006).Bellworthy, J. & Fine, M. Beyond peak summer temperatures, branching corals in the Gulf of Aqaba are resilient to thermal stress but sensitive to high light. Coral Reefs 36, 1071–1082 (2017).Article 
ADS 

Google Scholar 
Rex, A., Montebon, F. & Yap, H. T. Metabolic responses of the scleractinian coral Porites cylindrica Dana to water motion. I. Oxygen flux studies. J. Exp. Mar. Biol. Ecol. 186, 33–52 (1995).Article 

Google Scholar 
Long, M. H., Berg, P., de Beer, D. & Zieman, J. C. In situ coral reef oxygen metabolism: An eddy correlation study. PLoS ONE 8, e58581 (2013).Article 
ADS 
CAS 

Google Scholar 
Fabricius, K. E. & Klumpp, D. W. Widespread mixotrophy in reef-inhabiting soft corals: The influence of depth, and colony expansion and contraction on photosynthesis. Mar. Ecol. Prog. Ser. 125, 195–204 (1995).Article 
ADS 

Google Scholar 
Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248–254 (1976).Article 
CAS 

Google Scholar 
Raimonet, M., Guillou, G., Mornet, F. & Richard, P. Macroalgae δ15N values in well-mixed estuaries: Indicator of anthropogenic nitrogen input or macroalgae metabolism? Estuar. Coast. Shelf Sci. 119, 126–138 (2013).Article 
ADS 
CAS 

Google Scholar 
Furla, P., Galgani, I., Durand, I. & Allemand, D. Sources and mechanisms of inorganic carbon transport for coral calcification and photosynthesis. J. Exp. Biol. 203, 3445–3457 (2000).Article 
CAS 

Google Scholar 
Hughes, A. D., Grottoli, A. G., Pease, T. K. & Matsui, Y. Acquisition and assimilation of carbon in non-bleached and bleached corals. Mar. Ecol. Prog. Ser. 420, 91–101 (2010).Article 
ADS 
CAS 

Google Scholar 
Rau, G. H., Takahashi, T. & Des Marais, D. J. Latitudinal variations in plankton delta C-13—Implications for CO2 and productivity in past oceans. Nature 341, 516–518 (1989).Article 
ADS 
CAS 

Google Scholar 
McMahon, K. W., Hamady, L. L. & Thorrold, S. R. A review of ecogeochemistry approaches to estimating movements of marine animals. Limnol. Oceanogr. 58, 697–714 (2013).Article 
ADS 
CAS 

Google Scholar 
Muscatine, L., Porter, J. W. & Kaplan, I. R. Resource partitioning by reef corals as determined from stable isotope composition. Mar. Biol. 100, 185–193 (1989).Article 

Google Scholar 
Swart, P. K. et al. The isotopic composition of respired carbon dioxide in scleractinian corals: Implications for cycling of organic carbon in corals. Geochim. Cosmochim. Acta 69, 1495–1509 (2005).Article 
ADS 
CAS 

Google Scholar 
Rodrigues, L. J. & Grottoli, A. G. Calcification rate and the stable carbon, oxygen, and nitrogen isotopes in the skeleton, host tissue, and zooxanthellae of bleached and recovering Hawaiian corals. Geochim. Cosmochim. Acta 70, 2781–2789 (2006).Article 
ADS 
CAS 

Google Scholar 
Grottoli, A. G. & Rodrigues, L. J. Bleached Porites compressa and Montipora capitata corals catabolize δ13C-enriched lipids. Coral Reefs 30, 687–692 (2011).Article 
ADS 

Google Scholar 
Levas, S. J., Grottoli, A. G., Hughes, A., Osburn, C. L. & Matsui, Y. Physiological and biogeochemical traits of bleaching and recovery in the mounding species of coral porites lobata: Implications for resilience in mounding corals. PLoS ONE 8, 32–35 (2013).Article 

Google Scholar 
Schoepf, V. et al. Annual coral bleaching and the long-term recovery capacity of coral. Proc. R. Soc. B Biol. Sci. 282, 20151887 (2015).Article 

Google Scholar 
Lesser, M. P. et al. Nitrogen fixation by symbiotic cyanobacteria provides a source of nitrogen for the scleractinian coral Montastraea cavernosa. Mar. Ecol. Prog. Ser. 346, 143–152 (2007).Article 
ADS 
CAS 

Google Scholar 
Carpenter, E. J., Harvey, H. R., Brian, F. & Capone, D. G. Biogeochemical tracers of the marine cyanobacterium Trichodesmium. Deep Sea Res. I Oceanogr. Res. Pap. 44, 27–38 (1997).Article 
ADS 
CAS 

Google Scholar 
Lachs, L. et al. Effects of tourism-derived sewage on coral reefs: Isotopic assessments identify effective bioindicators. Mar. Pollut. Bull. 148, 85–96 (2019).Article 
CAS 

Google Scholar 
Kürten, B. et al. Influence of environmental gradients on C and N stable isotope ratios in coral reef biota of the Red Sea, Saudi Arabia. J. Sea Res. 85, 379–394 (2014).Article 
ADS 

Google Scholar 
Core Team, R. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).Article 
ADS 

Google Scholar 
Kassambara, A. ggpubr: ‘ggplot2’ Based Publication Ready Plots. R Package Version 0.4.0 (2020).Kassambara, A. rstatix: Pipe-Friendly Framework for Basic Statistical Tests. R Package Version 0.7.0 (2021).Contreras-Silva, A. I. et al. A meta-analysis to assess long-term spatiotemporal changes of benthic coral and macroalgae cover in the Mexican Caribbean. Sci. Rep. 10, 1–12 (2020).Article 

Google Scholar 
Ledlie, M. H. et al. Phase shifts and the role of herbivory in the resilience of coral reefs. Coral Reefs 26, 641–653 (2007).Article 
ADS 

Google Scholar 
Kuffner, I. B. & Toth, L. T. A geological perspective on the degradation and conservation of western Atlantic coral reefs. Conserv. Biol. 30, 706–715 (2016).Article 

Google Scholar 
Hughes, T. P. Catastrophes, phase shifts, and large-scale degradation of a Caribbean Coral Reef. Science 265, 1547–1551 (1994).Article 
ADS 
CAS 

Google Scholar 
de Bakker, D. M., Meesters, E. H., Bak, R. P. M., Nieuwland, G. & van Duyl, F. C. Long-term shifts in coral communities on shallow to deep reef slopes of Curaçao and Bonaire: Are there any winners? Front. Mar. Sci. 3, 247 (2016).Article 

Google Scholar 
Mergner, H. & Svoboda, A. Productivity and seasonal changes in selected reef areas in the Gulf of Aqaba (Red Sea). Helgoländer Meeresun. 30, 383–399 (1977).Article 

Google Scholar 
Schlichter, D., Svoboda, A. & Kremer, B. P. Functional autotrophy of Heteroxenia fuscescens (Anthozoa: Alcyonaria): Carbon assimilation and translocation of photosynthates from symbionts to host. Mar. Biol. 78, 29–38 (1983).Article 
CAS 

Google Scholar 
Al-Sofyani, A. A. & Niaz, G. R. A comparative study of the components of the hard coral Seriatopora hystrix and the soft coral Xenia umbellata along the Jeddah coast, Saudi Arabia. Rev. Biol. Mar. Oceanogr. 42, 207–219 (2007).Article 

Google Scholar 
McCloskey, L. R., Wethey, D. S. & Porter, J. W. Measurement and interpretation of photosynthesis and respiration in reef corals. In Coral Reefs: Research Methods (eds Stoddart, D. R. & Johannes, R. E.) 379–396 (United Nations Educational, Scientific and Cultural Organization, 1978).
Google Scholar 
Baker, D. M., Freeman, C. J., Wong, J. C. Y., Fogel, M. L. & Knowlton, N. Climate change promotes parasitism in a coral symbiosis. ISME J. 12, 921–930 (2018).Article 
CAS 

Google Scholar 
Hoegh-Guldberg, O. & Smith, G. J. The effect of sudden changes in temperature, light and salinity on the population density and export of zooxanthellae from the reef corals Stylophora pistillata Esper and Seriatopora hystrix Dana. J. Exp. Mar. Biol. Ecol. 129, 279–303 (1989).Article 

Google Scholar 
Iglesias-Prieto, R., Matta, J. L., Robins, W. A. & Trench, R. K. Photosynthetic response to elevated temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture. Proc. Natl. Acad. Sci. 89, 10302–10305 (1992).Article 
ADS 
CAS 

Google Scholar 
Béraud, E., Gevaert, F., Rottier, C. & Ferrier-Pagès, C. The response of the scleractinian coral Turbinaria reniformis to thermal stress depends on the nitrogen status of the coral holobiont. J. Exp. Biol. 216, 2665–2674 (2013).
Google Scholar 
Kremien, M., Shavit, U., Mass, T. & Genin, A. Benefit of pulsation in soft corals. Proc. Natl. Acad. Sci. U.S.A. 110, 8978–8983 (2013).Article 
ADS 
CAS 

Google Scholar 
Grover, R. et al. Coral uptake of inorganic phosphorus and nitrogen negatively affected by simultaneous changes in temperature and pH. PLoS ONE 6, 1–10 (2011).
Google Scholar 
Cardini, U. et al. Microbial dinitrogen fixation in coral holobionts exposed to thermal stress and bleaching. Environ. Microbiol. 18, 2620–2633 (2016).Article 
CAS 

Google Scholar 
Cardini, U. et al. Functional significance of dinitrogen fixation in sustaining coral productivity under oligotrophic conditions. Proc. R. Soc. B Biol. Sci. 282, 20152257 (2015).Article 

Google Scholar 
Santos, H. F. et al. Climate change affects key nitrogen-fixing bacterial populations on coral reefs. ISME J. 8, 2272–2279 (2014).Article 

Google Scholar 
Tilstra, A. et al. Relative diazotroph abundance in symbiotic red sea corals decreases with water depth. Front. Mar. Sci. 6, 372 (2019).Article 

Google Scholar 
Klinke, A. et al. Impact of phosphate enrichment on the susceptibility of the pulsating soft coral Xenia umbellata to ocean warming. Front. Mar. Sci. 9, 1026321 (2022).Article 

Google Scholar 
Rädecker, N. et al. Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling. ISME J. https://doi.org/10.1038/s41396-021-01158-8 (2021).Article 

Google Scholar 
Swart, P. K., Saied, A. & Lamb, K. Temporal and spatial variation in the δ15N and δ13C of coral tissue and zooxanthellae in Montastraea faveolata collected from the Florida reef tract. Limnol. Oceanogr. 50, 1049–1058 (2005).Article 
ADS 
CAS 

Google Scholar 
Grottoli, A. G., Tchernov, D. & Winters, G. Physiological and biogeochemical responses of super-corals to thermal stress from the Northern Gulf of Aqaba, Red Sea. Front. Mar. Sci. 4, 215 (2017).Article 

Google Scholar 
Dubinsky, Z. & Stambler, N. Marine pollution and coral reefs. Glob. Change Biol. 2, 511–526 (1996).Article 
ADS 

Google Scholar 
Loya, Y., Lubinevsky, H., Rosenfeld, M. & Kramarsky-Winter, E. Nutrient enrichment caused by in situ fish farms at Eilat, Red Sea is detrimental to coral reproduction. Mar. Pollut. Bull. 49, 344–353 (2004).Article 
CAS 

Google Scholar 
Costa, O. S., Nimmo, M. & Attrill, M. J. Coastal nutrification in Brazil: A review of the role of nutrient excess on coral reef demise. J. S. Am. Earth Sci. 25, 257–270 (2008).Article 

Google Scholar 
Tait, D. R. et al. The influence of groundwater inputs and age on nutrient dynamics in a coral reef lagoon. Mar. Chem. 166, 36–47 (2014).Article 
CAS 

Google Scholar 
Guan, Y., Hohn, S., Wild, C. & Merico, A. Vulnerability of global coral reef habitat suitability to ocean warming, acidification and eutrophication. Glob. Change Biol. 26, 5646–5660 (2020).Article 
ADS 

Google Scholar 
Hall, E. R. et al. Eutrophication may compromise the resilience of the Red Sea coral Stylophora pistillata to global change. Mar. Pollut. Bull. 131, 701–711 (2018).Article 
CAS 

Google Scholar 
Naumann, M. S. et al. Organic matter release by dominant hermatypic corals of the Northern Red Sea. Coral Reefs 29, 649–659 (2010).Article 
ADS 

Google Scholar 
Wild, C. et al. Coral mucus functions as an energy carrier and particle trap in the reef ecosystem. Nature 428, 66–70 (2004).Article 
ADS 
CAS 

Google Scholar  More

Zhang, Z.-Q. Phylum Athropoda. Zootaxa 3703, 17 (2013).Article 

Google Scholar 
Christenhusz, M. J. M. & Byng, J. W. The number of known plants species in the world and its annual increase. Phytotaxa 261, 201 (2016).Article 

Google Scholar 
Forbes, A. A., Bagley, R. K., Beer, M. A., Hippee, A. C. & Widmayer, H. A. Quantifying the unquantifiable: why Hymenoptera, not Coleoptera, is the most speciose animal order. BMC Ecol 18, 21 (2018).Article 

Google Scholar 
Glor, R. E. Phylogenetic Insights on Adaptive Radiation. Annu. Rev. Ecol. Evol. Syst. 41, 251–270 (2010).Article 

Google Scholar 
Schluter, D. The ecology of adaptive radiation. (Oxford Univ Press, 2000).Simpson, G. G. Tempo and mode in evolution. (Columbia Univ Press, 1944).Gavrilets, S. & Losos, J. B. Adaptive Radiation: Contrasting Theory with Data. Science 323, 732–737 (2009).Article 
CAS 

Google Scholar 
Losos, J. B. Adaptive Radiation, Ecological Opportunity, and Evolutionary Determinism: American Society of Naturalists E. O. Wilson Award Address. Am. Nat. 175, 623–639 (2010).Article 

Google Scholar 
Hodges, S. A. & Arnold, M. L. Spurring plant diversification: are floral nectar spurs a key innovation? Proc. R Soc. B: Biol. Sci. 262, 343–348 (1995).Article 

Google Scholar 
Hunter, J. P. & Jernvall, J. The hypocone as a key innovation in mammalian evolution. Proc. Natl. Acad. Sci. U.S.A. 92, 10718–10722 (1995).Article 
CAS 

Google Scholar 
Grant, P. R. Ecology and Evolution of Darwin’s Finches. (Princeton Univ Press, 1986).Erwin, D. H. The end and the beginning: recoveries from mass extinctions. Trend. Ecol. Evol. 13, 344–349 (1998).Article 
CAS 

Google Scholar 
Jablonski, D. Lessons from the past: Evolutionary impacts of mass extinctions. Proc. Natl. Acad. Sci. U.S.A. 98, 5393–5398 (2001).Article 
CAS 

Google Scholar 
Donoghue, M. J. & Sanderson, M. J. Confluence, synnovation, and depauperons in plant diversification. New Phytol. 207, 260–274 (2015).Article 

Google Scholar 
Pie, M. R. & Feitosa, R. S. M. Relictual ant lineages and their evolutionary implications. Myrmecol News 22, 55–58 (2016).
Google Scholar 
Eldredge, N. & Stanley, S. M. Living Fossils (Casebooks in Earth Sciences). (Springer, 1984).Alfaro, M. E. et al. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. 106, 13410–13414 (2009).Article 
CAS 

Google Scholar 
Magallón, S., Sánchez-Reyes, L. L. & Gómez-Acevedo, S. L. Thirty clues to the exceptional diversification of flowering plants. Ann. Botany 123, 491–503 (2019).Article 

Google Scholar 
Hunter, J. P. Key innovations and the ecology of macroevolution. Trend. Ecol. Evol. 13, 31–36 (1998).Article 
CAS 

Google Scholar 
Wellborn, G. A. & Langerhans, R. B. Ecological opportunity and the adaptive diversification of lineages. Ecol. Evol. 5, 176–195 (2015).Article 

Google Scholar 
Gould, S. J. & Vrba, E. S. Exaptation—a Missing Term in the Science of Form. Paleobiology 8, 4–15 (1982).Article 

Google Scholar 
Eldredge, N. Simpson’s Inverse: Bradytely and the Phenomenon of Living Fossils. in Living Fossils (eds. Eldredge, N. & Stanley, S. M.) 272–277 (Springer New York, 1984). https://doi.org/10.1007/978-1-4613-8271-3_34.Nagalingum, N. S. et al. Recent Synchronous Radiation of a Living Fossil. Science 334, 796–799 (2011).Article 
CAS 

Google Scholar 
Schopf, T. J. M. Rates of Evolution and the Notion of ‘Living Fossils’. Annu. Rev. Earth Planet. Sci. 12, 245–292 (1984).Article 

Google Scholar 
Czekanski-Moir, J. E. & Rundell, R. J. The Ecology of Nonecological Speciation and Nonadaptive Radiations. Trend. Ecol. Evol. 34, 400–415 (2019).Article 

Google Scholar 
Olson, M. E. & Arroyo-Santos, A. Thinking in continua: beyond the “adaptive radiation” metaphor. BioEssays 31, 1337–1346 (2009).Article 

Google Scholar 
Barnes, B. D., Sclafani, J. A. & Zaffos, A. Dead clades walking are a pervasive macroevolutionary pattern. Proc. Natl. Acad. Sci. USA 118, e2019208118 (2021).Article 
CAS 

Google Scholar 
Quental, T. B. & Marshall, C. R. How the Red Queen Drives Terrestrial Mammals to Extinction. Science 341, 290–292 (2013).Article 
CAS 

Google Scholar 
Strathmann, R. R. & Slatkin, M. The improbability of animal phyla with few species. Paleobiology 9, 97–106 (1983).Article 

Google Scholar 
Darwin, C. On the origin of species by means of natural selection. (J. Murray, 1859).Kase, T. & Hayami, I. Unique submarine cave mollusc fauna: composition, origin and adaptation. J. Mollus Stud. 58, 446–449 (1992).Article 

Google Scholar 
Tunnicliffe, V. The Nature and Origin of the Modern Hydrothermal Vent Fauna. PALAIOS 7, 338 (1992).Article 

Google Scholar 
Oji, T. Is predation intensity reduced with increasing depth? Evidence from the west Atlantic stalked crinoid Endoxocrinus parrae (Gervais) and implications for the Mesozoic marine revolution. Paleobiology 22, 339–351 (1996).Article 

Google Scholar 
Oji, T. & Okamoto, T. Arm autotomy and arm branching pattern as anti-predatory adaptations in stalked and stalkless crinoids. Paleobiology 20, 27–39 (1994).Article 

Google Scholar 
Rest, J. S. et al. Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Mol. Phyl. Evol. 29, 289–297 (2003).Article 
CAS 

Google Scholar 
Rabosky, D. L. & Benson, R. B. J. Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data. Nat. Commun. 12, 2945 (2021).Article 
CAS 

Google Scholar 
Louca, S., Henao‐Diaz, L. F. & Pennell, M. The scaling of diversification rates with age is likely explained by sampling bias. Evolution 76, 1625–1637 (2022).Article 

Google Scholar 
Qian, H. & Zhang, J. Using an updated time-calibrated family-level phylogeny of seed plants to test for non-random patterns of life forms across the phylogeny: Phylogeny of seed plant families. J. Syst. Evol. 52, 423–430 (2014).Article 

Google Scholar 
The Plant List. Version 1.1. http://www.theplantlist.org/.Jetz, W. & Pyron, R. A. The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life. Nat. Ecol. Evol. 2, 850–858 (2018).Article 

Google Scholar 
Tonini, J. F. R., Beard, K. H., Ferreira, R. B., Jetz, W. & Pyron, R. A. Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status. Biol. Conservation 204, 23–31 (2016).Article 

Google Scholar 
Faurby, S. et al. PHYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology. Ecology 99, 2626–2626 (2018).Article 

Google Scholar 
IUCN. IUCN red List of Threatened Species. Version 2017.3. Retrieved from https://www.iucnredlist.org. Downloaded on May 14, 2020. (2017).Magallon, S. & Sanderson, M. J. Absolute diversification rates in angiosperm clades. Evolution 55, 1762–1780 (2001).CAS 

Google Scholar 
Raup, D. M. Mathematical models of cladogenesis. Paleobiology 11, 42–52 (1985).Article 

Google Scholar 
Kembel, S. W. et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464 (2010).Article 
CAS 

Google Scholar 
Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).Article 

Google Scholar 
Vilela, B. & Villalobos, F. letsR: a new R package for data handling and analysis in macroecology. Methods Ecol. Evol. 6, 1229–1234 (2015).Article 

Google Scholar 
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Retrieved from https://www.R-project.org/. (2020).Garnier, S. viridis: Default Color Maps from ‘matplotlib’. Version 0.5.1. Available in https://CRAN.R-project.org/package=viridis (2018).Bivand, R. et al. rgdal: Bindings for the ‘Geospatial’ Data Abstraction Library. Version 1.5.32. Available in https://CRAN.R-project.org/package=rgdal (2020). More

Seebens, H. et al. No saturation in the accumulation of alien species worldwide. Nat. Commun. 8, 14435 (2017).Article 
CAS 

Google Scholar 
Pimentel, D., Zuniga, R. & Morrison, D. Update on the environmental and economic costs associated with alien-invasive species in the United States. Ecol. Econ. 52, 273–288 (2005).Article 

Google Scholar 
Simberloff, D. & Von Holle, B. Positive interactions of nonindigenous species: invadsional meltdown? Biol. Invasions 1, 21–32 (1999).Article 

Google Scholar 
Montgomery, W. I., Lundy, M. G. & Reid, N. ‘Invasional meltdown’: evidence for unexpected conseuences and cumulative impacts of multispecies invasions. Biol. Invasions 14, 1111–1115 (2012).Article 

Google Scholar 
Jackson, M. C. Interactions among multiple invasive animals. Ecology 96, 2035–2041 (2015).Article 
CAS 

Google Scholar 
Braga, R. R. et al. Invasional meltdown: an experimental test and a framework to distinguish synergistic, additive, and antagonistic effects. Hydrobiologia 847, 1603–1618 (2020).Article 

Google Scholar 
Crooks, K. R. & Soulé, M. E. Mesopredator release and avifaunal extinctions in a fragmented system. Nature 400, 563–566 (1999).Article 
CAS 

Google Scholar 
Klemmer, A. J., Wissinger, S. A., Greig, H. S. & Ostrofsky, M. L. Nonlinear effects of consumer density on multiple ecosystem processes. J. Anim. Ecol. 81, 779–780 (2012).Article 

Google Scholar 
De Meester, L., Vanoverbeke, J., Kilsdonk, L. J. & Urban, M. C. Evolving perspectives on monopolization and priority effects. Trends Ecol. Evol. 31, 136–146 (2016).Article 

Google Scholar 
Vitousek, P. M., D’Antonio, C. M., Loope, L. L. & Westbrooks, R. Biological invasions as global environmental change. Am. Sci. 84, 468–478 (1996).
Google Scholar 
McKinney, M. L. & Lockwood, J. L. Biotic homogenization: a few winners replacing many losers in the next mass extinction. Trends Ecol. Evol. 14, 450–453 (1999).Article 
CAS 

Google Scholar 
Liebig, J. et al. Bythotrephes longimanus: U.S. Geological Survey, Nonindigenous Aquatic Species Database (2021). Available at: https://nas.er.usgs.gov/queries/factsheet.aspx?SpeciesID=162.Benson, A.J. et al. Dreissena polymorpha (Pallas, 1771): U.S. Geological Survey, Nonindigenous Aquatic Species Database (2021). Available at: https://nas.er.usgs.gov/queries/FactSheet.aspx?speciesID=5Stewart, T. J., Johannsson, O. E., Holeck, K., Sprules, W. G. & O’Gorman, R. The Lake Ontario zooplankton community before (1987-1991) and after (2001-2005) invasion-induced ecosystem change. J. Gt. Lakes Res. 36, 596–605 (2010).Article 

Google Scholar 
Strecker, A. L. et al. Direct and indirect effects of an invasive planktonic predator on pelagic food webs. Limnol. Oceanogr. 56, 179–192 (2011).Article 

Google Scholar 
Karatayev, A. Y., Burlakova, L. E. & Padilla, D. K. Zebra versus quagga mussels: a review of their spread, population dynamics, and ecosystem impacts. Hydrobiologia 746, 97–112 (2015).Article 
CAS 

Google Scholar 
Kerfoot, W. C. et al. A plague of waterfleas (Bythotrephes): impacts on microcrustacean community structure, seasonal biomass, and secondary production in a large inland-lake complex. Biol. Invasions 18, 1121–1145 (2016).Article 

Google Scholar 
Strayer, D. et al. Long-term variability and density dependence in Hudson River Dreissena populations. Freshw. Biol. 65, 474–489 (2019).Article 

Google Scholar 
Fang, X., Stefan, H. G., Jiang, L., Jacobson, P. C. & Pereira D. L. Projected impacts of climatic changes on cisco oxythermal habitat in Minnesota lakes and management strategies in Handbook of Climate Change mitigation and Adaptation (eds. Chen, W.-Y., Suzuki, T. & Lackner, M.) 657-722 (Springer, 2015).Stefan, H. G., Hondzo, M., Fang, X., Eaton, J. G. & McCormick, J. H. Simulated long-term temperature and dissolved oxygen characteristics of lakes in the north-central United States and associated fish habitat limits. Limnol. Oceanogr. 41, 1124–1135 (1996).Article 

Google Scholar 
Jacobson, P. C., Jones, T. S., Rivers, P. & Pereira, D. L. Field estimation of a lethal oxythermal niche boundary for adult ciscoes in Minnesota lakes. T. Am. Fish. Soc. 137, 1464–1474 (2008).Article 

Google Scholar 
Hecky, R. E. et al. The nearshore phosphorus shunt: a consequence of ecosystem engineering by dreissenids in the Laurentian Great Lakes. Can. J. Fish. Aquat. Sci. 61, 1285–1293 (2004).Article 
CAS 

Google Scholar 
Sousa, R., Gutiérrez, J. L. & Aldridge, D. C. Non-indigenous invasive bivalves as ecosystem engineers. Biol. Invasions 11, 2367–2385 (2009).Article 

Google Scholar 
Higgins, S. N. & Vander Zanden, M. J. What a difference a species makes: a meta-analysis of dreissenid mussel impacts on freshwater ecosystems. Ecol. Monogr. 80, 179–196 (2010).Article 

Google Scholar 
Mayer, C. M. et al. Benthification of Freshwater Lakes: Exotic Mussels Turning Ecosystems Upside Down in Quagga and Zebra Mussels: Biology, Impacts, and Control, 2nd ed. (eds. Nalepa, T. F. & Schloesser D. W.) 575-586 (CRC Press, 2014).Lehman, J. T. & Cárcres, C. E. Food-web responses to species invasion by a predatory invertebrate: Bythotrephes in Lake Michigan. Limnol. Oceanogr. 38, 879–891 (1993).Article 

Google Scholar 
Bunnell, D. B., Keeler, K. M., Puchala, E. A., Davis, B. M. & Pothoven, S. A. Comparing seasonal dynamics of the Lake Huron zooplankton community between 1983-1984 and 2007 and revisiting the impact of Bythotrephes planktivory. J. Gt. Lakes Res. 38, 451–462 (2012).Article 

Google Scholar 
Pawlowski, M. B., Branstrator, D. K., Hrabik, T. R. & Sterner, R. W. Changes in the cladoceran community of Lake Superior and thee role of Bythotrephes longimanus. J. Gt. Lakes Res. 43, 1101–1110 (2017).Article 

Google Scholar 
Hoffman, J. C., Smith, M. E. & Lehman, J. T. Perch or plankton: top-down control of Daphnia by yellow perch (Perca flavescens) or Bythotrephes cederstroemi in an inland lake? Freshw. Biol. 46, 759–775 (2001).Article 

Google Scholar 
Bunnell, D. B., Davis, B. M., Warner, D. M., Chriscinske, M. A. & Roseman, E. F. Planktivory in the changing Lake Huron zooplankton community: Bythotrephes consumption exceeds that of Mysis and fish. Freshw. Biol. 56, 1281–1296 (2011).Article 

Google Scholar 
Merkle, C. & De Stasio, B. Bythotrephes longimanus in shallow, nearshore waters: interactions with Leptodora kindtii, impacts on zooplankton, and implications for secondary dispersal from southern Green Bay, Lake Michigan. J. Gt. Lakes Res. 44, 934–942 (2018).Article 

Google Scholar 
Walsh, J. R., Carpenter, S. R. & Vander Zanden, M. J. Invasive species triggers a massive loss of ecosystem services through a trophic cascade. Proc. Natl. Acad. Sci. USA 113, 4081–4085 (2016).Article 
CAS 

Google Scholar 
Lehman, J. T. Algal biomass unaltered by food-web changes in Lake Michigan. Nature 332, 537–538 (1988).Article 

Google Scholar 
Wahlström, E. & Westman, E. Planktivory by the predacious cladoceran Bythotrephes longimanus: effects on zooplankton size structure and density. Can. J. Fish. Aquat. Sci. 56, 1865–1872 (1999).Article 

Google Scholar 
Strecker, A. L. & Arnott, S. E. Invasive predator, Bythotrephes, has varied effects on ecosystem function in freshwater lakes. Ecosystems 11, 490–503 (2008).Article 

Google Scholar 
Benke, A. C. Concepts and patterns of invertebrate production in running waters. Verh. Int. Theor. Angew. Limnol. 25, 15–38 (1993).
Google Scholar 
Jones, T. & Montz, G. Population increase and associated effects of zebra mussels Dreissena polymorpha in Lake Mille Lacs, Minnesota, U.S.A. Bioinvasion Rec. 9, 772–792 (2020).Article 

Google Scholar 
Strayer, D. L. & Malcom, H. M. Long-term demography of a zebra mussel (Dreissena polymorpha) population. Freshw. Biol. 51, 117–130 (2006).Article 

Google Scholar 
Geisler, M. E., Rennie, M. D., Gillis, D. M. & Higgins, S. N. A predictive model for water clarity following dreissenid invasion. Biol. Invasions 18, 1989–2006 (2016).Article 

Google Scholar 
Barbiero, R. P. & Tuchman, M. L. Long-term dreissenid impacts on water clarity in Lake Erie. J. Gt. Lakes Res. 30, 557–565 (2004).Article 

Google Scholar 
Fishman, D. B., Adlerstein, S. A., Vanderploeg, H. A., Fahnenstiel, G. L. & Scavia, D. Causes of phytoplankton changes in Saginaw Bay, Lake Huron, during the zebra mussel invasion. J. Gt. Lakes Res. 35, 482–495 (2009).Article 

Google Scholar 
Zhang, H., Culver, D. A. & Boegman, L. Dreissenids in Lake Erie: an algal filter or a fertilizer? Aquat. Invasions 6, 175–194 (2011).Article 

Google Scholar 
Higgins, S. N., Vander Zanden, M. J., Joppa, L. N. & Vadeboncoeur, Y. The effect of dreissenid invasions on chlorophyll and the chlorophyll: total phosphorus ration in north-temperate lakes. Can. J. Fish. Aquat. Sci. 68, 319–329 (2011).Article 
CAS 

Google Scholar 
Lehman, J. T. & Branstrator, D. K. A model for growth, development, and diet selection by the invertebrate predator Bythotrephes cederstroemi. J. Gt. Lakes Res. 21, 610–619 (1995).Article 

Google Scholar 
Azan, S. S. E., Arnott, S. E. & Yan, N. D. A review of the effects of Bythotrephes longimanus and calcium decline on zooplankton communities – can interactive effects be predicted? Environ. Rev. 23, 395–413 (2015).Article 
CAS 

Google Scholar 
Pangle, K. L., Peacor, S. D. & Johannsson, O. E. Large nonlethal effects of an invasive invertebrate predator on zooplankton population growth rate. Ecology 88, 402–412 (2007).Article 

Google Scholar 
Cross, T. K. & Jacobson, P. C. Landscape factors influencing lake phosphorus concentrations across Minnesota. Lake Reserv Manag 29, 1–12 (2013).Article 
CAS 

Google Scholar 
McQueen, D. J., Johannes, M. R. S., Post, J. R., Stewart, T. J. & Lean, D. R. S. Bottom-up and top-down impacts on freshwater pelagic community structure. Ecol. Monogr. 59, 289–309 (1989).Article 

Google Scholar 
Mills, E. L. et al. Lake Ontario: food web dynamics in a changing ecosystem (1970-2000). Can. J. Fish. Aquat. Sci. 60, 471–490 (2003).Article 

Google Scholar 
Lehman, J. T. Causes and consequences of cladoceran dynamics in Lake Michigan: implications of species invasion by. Bythotrephes. J. Gt. Lakes Res. 17, 437–445 (1991).Article 

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

Google Scholar 
Brooks, J. L. & Dodson, S. I. Predation, body size, and composition of plankton. Science 150, 28–35 (1965).Article 
CAS 

Google Scholar 
Rennie, M. D., Evans, D. O. & Young, J. D. Increased dependence on nearshore benthic resources in the Lake Simcoe ecosystem after dreissenid invasion. Inland Waters 3, 297–310 (2013).Article 

Google Scholar 
Goto, D., Dunlop, E. S., Young, J. D. & Jackson, D. A. Shifting trophic control of fishery-ecosystem dynamics following biological invasions. Ecol. Appl. 30, e02190 (2020).Article 

Google Scholar 
Hansen, G. J. A. et al. Walleye growth declines following zebra mussel and Bythotrephes invasion. Biol. Invasions 22, 1481–1495 (2020).Article 

Google Scholar 
Yan, N. & Pawson, T. Changes in the crustacean zooplankton community of Harp Lake, Canada, following invasion by. Bythotrephes cederstrœmi. Freshw. Biol. 37, 409–425 (1997).Article 

Google Scholar 
Bourdeau, P. E., Bach, M. T. & Peacor, S. D. Predator presence dramatically reduces copepod abundance through condition-mediated non-consumptive effects. Freshw. Biol. 61, 1020–1031 (2016).Article 
CAS 

Google Scholar 
Lehman, J. R. Ecological principles affecting community structure and secondary production by zooplankton in marine and freshwater environments. Limnol. Oceanogr. 33, 931–945 (1988).
Google Scholar 
Walsh, J. R., Lathrop, R. C., & Vander Zanden, M.J.Invasive invertebrate predator, Bythotrephes longimanus, reverses trophic cascade in a north-temperate lake. Limnol. Oceanogr. 62, 2498–2509 (2017).Article 

Google Scholar 
Underwood, A. J. On beyond BACI: sampling designs that might reliably detect environmental disturbances. Ecol. Appl. 4, 3–15 (1994).Article 

Google Scholar 
Sala, O. E. et al. Global biodiversity scenarios for the year 2100. Science 287, 1770–1774 (2000).Article 
CAS 

Google Scholar 
Strayer, D. L., Eviner, V. T., Jeschke, J. M. & Pace, M. L. Understanding the long-term effects of species invasions. Trends Ecol. Evol. 21, 645–651 (2006).Article 

Google Scholar 
Magnuson, J. J. Long-term ecological research and the invisible present. BioScience 40, 495–501 (1990).Article 

Google Scholar 
Doak, D. F. et al. Understanding and predicting ecological dynamics: are major surprises inevitable? Ecology 89, 952–961 (2008).Article 

Google Scholar 
Hansen, G. J. A., Gaeta, J. W., Hansen, J. F. & Carpenter, S. R. Learning to manage and managing to learn: sustaining freshwater recreational fisheries in a changing environment. Fisheries 40, 56–64 (2015).Article 

Google Scholar 
Dumont, H. J., Van De Velde, I. & Dumont, S. The dry weight estimate of biomass in a selection of Cladocera, Copepoda and Rotifera from the plankton, periphyton and benthos of continental waters. Oecologia 19, 75–97 (1975).Article 

Google Scholar 
Culver, D. A., Boucherle, M. M., Bean, D. J. & Fletcher, J. W. Biomass of freshwater crustacean zooplankton from length-weight regressions. Can. J. Fish. Aquat. Sci. 42, 1380–1390 (1985).Article 

Google Scholar 
Manly, B. F. J. Randomization, bootstrap and Monet Carlo methods in biology, 3rd ed. (Chapman and Hall/CRC, 2007).Arar, E. J. Method 446.0. In vitro determination of chlorophylls a, b, c1 + c2 and pheopigments in marine and freshwater algae by visible spectrophotometry, revision 1.2. (U.S. Environmental Protection Agency, 1997).O’Dell, J. W. Method 365.1 Determination of phosphorus by semi-automated colorimetry, revision 2.0. (U.S. Environmental Agency, 1993).Helsel, D. R. & Hirsch, R. M. Statistical methods in water resources (U. S. Geological Survey, 2002).Minnesota Pollution Control Agency (MPCA). Surface water data. https://webapp.pca.state.mn.us/wqd/surface-water (MPCA, 2021).Read, J. S. et al. Data release: Process-based predictions of lake water temperature in the Midwest US: U.S. Geological Survey data release, https://doi.org/10.5066/P9CA6XP8 (USGS, 2021).Hothorn, T., Hornik, K., van de Wiel, M. A. & Zeileis, A. Lego system for conditional inference. Am. Stat. 60, 257–263 (2006).Article 

Google Scholar 
Dewitz, J. National Land Cover Database (NLCD) 2016 Products: U.S. Geological Survey data release, https://doi.org/10.5066/P96HHBIE (USGS, 2019).Use of Fishes in Research Committee. Guidelines for the use of fishes in research. (American Fisheries Society, 2014)Pedersen, E. J., Miller, D. L., Simpson, G. L. & Ross, N. Hierarchical generalized additive models in ecology: an introduction with mgcv. PeerJ 7, e6876 (2019).Article 

Google Scholar 
Minnesota Geospatial Commons. DNR Hydrology Dataset. (2022). Available at: https://gisdata.mn.gov/dataset/water-dnr-hydrography.Minnesota Geospatial Commons. Lake Bathymetric Outlines, Contours, and DEM. (2021). Available at: https://gisdata.mn.gov/dataset/water-lake-bathymetry.ESRI ArcGIS Desktop: Release 10.6. Redlands, CA: Environmental Systems Research Institute (2018).Wood, S. N. Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J. R. Stat. Soc. 73, 3–36 (2011).Article 

Google Scholar 
Guerrero, F. & Rodríguez, V. Secondary production of a congeneric species assemblage of Acartia (Copepoda: Calanoida): a calculation based on the size-frequency distribution. Sci. Mar. 58, 161–167 (1994).
Google Scholar 
Cross, W. F. et al. Ecosystem ecology meets adaptive management: food web response to a controlled flood on the Colorado River, Glen Canyon. Ecol. Appl. 21, 2016–2033 (2011).Article 

Google Scholar 
Gillooly, J. F. Effect of body size and temperature on generation time in zooplankton. J. Plankton Res. 22, 241–251 (2000).Article 

Google Scholar 
Benke, A. C. & Huryn, A. D. Secondary production and quantitative food webs in Methods in Stream Ecology, Volume 2: ecosystem function (eds. Lamberti, G.A. & Hauer, F. R.) 235-254 (Academic Press, 2017).Wu, L. & Culver, D. A. Zooplankton grazing and phytoplankton abundance: an assessment before and after invasion of Dreissena polymorpha. J. Gt. Lakes Res. 17, 425–436 (1991).Article 

Google Scholar 
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing (Vienna, Austria, 2020). Accessible at: https://www.R-project.org/Minnesota Geospatial Commons. State Boundary. (2013). Available at: https://gisdata.mn.gov/dataset/bdry-state-of-minnesota.United States Geological Survey. North America Political Boundaries. (2006). Available at: https://www.sciencebase.gov/catalog/item/4fb555ebe4b04cb937751db9. More

Bovet, D. & Vauclair, J. Picture recognition in animals and humans. Behav. Brain. Res. 109, 143–165 (2000).Article 
CAS 

Google Scholar 
Anonymous. Tinder for Orangutans. Dublin Zoo. https://www.dublinzoo.ie/news/tinder-for-orangutans (2020).Henley, J. “Tinder for Orangutans”: Dutch zoo to let female choose mate on a tablet. The Guardian. https://www.theguardian.com/environment/2017/jan/31/tinder-for-orangutans-dutch-zoo-to-let-female-choose-mate-on-a-tablet (2017).Gierszewski, S. et al. The virtual lover: variable and easily guided 3D fish animations as an innovative tool in mate-choice experiments with sailfin mollies-II validation. Curr. Zool. 6, 65–74 (2017).Article 

Google Scholar 
Dolins, F. L., Klimowicz, C., Kelley, J. & Menzel, C. R. Using virtual reality to investigate comparative spatial cognitive abilities in chimpanzees and humans. Am. J. Primat. 76, 496–513 (2014).Article 

Google Scholar 
Faria, J. J. et al. A novel method for investigating the collective behaviour of fish: Introducing ‘Robofish’. Behav. Ecol. Sociobiol. 64, 1211–1218 (2010).Article 

Google Scholar 
Kozak, E. C. & Uetz, G. W. Male courtship signal modality and female mate preference in the wolf spider Schizocosa ocreata: results of digital multimodal playback studies. Curr. Zool. 65, 705–711 (2019).Article 

Google Scholar 
Loukola, O. J., Perry, C. J., Coscos, L. & Chittka, L. Bumblebees show cognitive flexibility by improving on an observed complex behavior. Science 355, 833–836 (2017).Article 
ADS 
CAS 

Google Scholar 
MacLaren, R. D. Evidence of an emerging female preference for an artificial male trait and the potential for spread via mate choice copying in Poecilia latipinna. Ethology 125, 575–586 (2019).
Google Scholar 
Rönkä, K. et al. Geographic mosaic of selection by avian predators on hindwing warning colour in a polymorphic aposematic moth. Ecol. Lett. 23, 1654–1663 (2020).Article 

Google Scholar 
Rosenthal, G. G., Rand, A. S. & Ryan, M. J. The vocal sac as a visual cue in anuran communication: An experimental analysis using video playback. Anim. Behav. 68, 55–58 (2004).Article 

Google Scholar 
Thurley, K. & Ayaz, A. Virtual reality systems for rodents. Curr. Zool. 63, 109–119 (2017).Article 

Google Scholar 
Ware, E. L., Saunders, D. R. & Troje, N. F. Social interactivity in pigeon courtship behavior. Curr. Zool. 63, 85–95 (2017).Article 

Google Scholar 
Wang, D. et al. The influence of model quality on self-other mate choice copying. Pers. Ind. Diff. 17, 110481 (2021).Article 

Google Scholar 
Gray, J. R., Pawlowski, V. & Willis, M. A. A method for recording behavior and multineuronal CNS activity from tethered insects flying in virtual space. J. Neurosci. Meth. 120, 211–223 (2002).Article 

Google Scholar 
Strauss, R., Schuster, S. & Götz, K. G. Processing of artificial visual feedback in the walking fruit fly Drosophila melanogaster. J. Exp. Biol. 200, 1281–1296 (1997).Article 
CAS 

Google Scholar 
Kemppainen, J. et al. Binocular mirror-symmetric microsaccadic sampling enables Drosophila hyperacute 3D vision. PNAS 119, e2109717119 (2022).Article 
CAS 

Google Scholar 
Bowers, R. I., Place, S. S., Todd, P. M., Penke, L. & Asendorpf, J. B. Generalization in mate-choice copying in humans. Behav. Ecol. 23, 112–124 (2012).Article 

Google Scholar 
Pruett-Jones, S. Independent versus nonindependent mate choice: do females copy each other? Am. Nat. 140, 1000–1006 (1992).Article 
CAS 

Google Scholar 
Dagaeff, A.-C., Pocheville, A., Nöbel, S., Isabel, G. & Danchin, E. Drosophila mate copying correlates with atmospheric pressure in a speed learning situation. Anim. Behav. 121, 163–174 (2016).Article 

Google Scholar 
Mery, F. et al. Public versus personal information for mate copying in an invertebrate. Curr. Biol. 19, 730–734 (2009).Article 
CAS 

Google Scholar 
Danchin, E. et al. Cultural flies: Conformist social learning in fruitflies predicts long-lasting mate-choice traditions. Science 362, 1025–1030 (2018).Article 
ADS 
CAS 

Google Scholar 
Monier, M., Nöbel, S., Isabel, G. & Danchin, E. Effects of a sex ratio gradient on female mate-copying and choosiness in Drosophila melanogaster. Curr. Zool. 64, 251–258 (2018).Article 

Google Scholar 
Monier, M., Nöbel, S., Danchin, E. & Isabel, G. Dopamine and serotonin are both required for mate-copying in Drosophila melanogaster. Front. Behav. Neurosci. 12, 334 (2019).Article 

Google Scholar 
Nöbel, S., Allain, M., Isabel, G. & Danchin, E. Mate copying in Drosophila melanogaster males. Anim. Behav. 141, 9–15 (2018).Article 

Google Scholar 
Nöbel, S., Danchin, E. & Isabel, G. Mate-copying for a costly variant in Drosophila melanogaster females. Behav. Ecol. 29, 1150–1156 (2018).Article 

Google Scholar 
Dukas, R. Natural history of social and sexual behavior in fruit flies. Sci. rep. 10, 1–11 (2020).Article 

Google Scholar 
Chouinard-Thuly, L. et al. Technical and conceptual considerations for using animated stimuli in studies of animal behavior. Curr. Zool. 63, 5–19 (2017).Article 

Google Scholar 
Nöbel, S. et al. Female fruit flies copy the acceptance, but not the rejection, of a mate. Behav. Ecol. 33, 1018–1024 (2022)Article 

Google Scholar 
Bretman, A., Westmancoat, J. D., Gage, M. J. G. & Chapman, T. Males use multiple, redundant cues to detect mating rivals. Curr. Biol. 21, 617–622 (2011).Article 
CAS 

Google Scholar 
Greenspan, R. J. & Ferveur, J. F. Courtship in drosophila. Ann. Rev. Gen. 34, 205 (2000).Article 
CAS 

Google Scholar 
Grillet, M., Dartevelle, L. & Ferveur, J. F. A Drosophila male pheromone affects female sexual receptivity. Proc. Roy. Soc. B. 273, 315–323 (2006).Article 
CAS 

Google Scholar 
Borst, A. Drosophila’s view on insect vision. Curr. Biol. 19, R36–R47 (2009).Article 
CAS 

Google Scholar 
Paulk, A., Millard, S. & van Swinderen, B. Vision in Drosophila: Seeing the world through a model´s eye. Ann. Rev. Entomol. 58, 313–332 (2013).Article 
CAS 

Google Scholar 
Antony, C. & Jallon, J. M. The chemical basis for sex recognition in Drosophila melanogaster. J. Insect. Physiol. 28, 873–880 (1982).Article 
CAS 

Google Scholar 
Keesey, I. W. et al. Adult frass provides a pheromone signature for Drosophila feeding and aggregation. J. Chem. Ecol. 42, 739–747 (2016).Article 
CAS 

Google Scholar 
Talyn, B. C. & Bowse, H. B. The role of courtship song in sexual selection and species recognition by female Drosophila melanogaster. Anim. Behav. 68, 1165–1180 (2004).Article 

Google Scholar 
von Schilcher, F. The function of pulse song and sine song in the courtship of Drosophila melanogaster. Anim. Behav. 24, 622–6251976 (1976).Article 

Google Scholar 
McGregor, P. K. et al. Design of playback experiments: The Thornbridge hall NATO ARW consensus. In Playback and Studies of Animal Communication (ed. McGregor, P.) 1–9 (Plenum Press, New York, 1992).Chapter 

Google Scholar 
Richmond, J. The three Rs. In The UFAW Handbook on the Care and Management of Laboratory and Other Research Animals (eds Hubrecht, R. & Kirkwood, J.) 5–22 (Wiley-Blackwell, Hoboken, 2002).
Google Scholar 
Russell, W. M. S. & Burch, R. L. The Principles of Humane Experimental Technique (Methuen & Co Ltd, 1959).
Google Scholar 
Schlupp, I., Ryan, M. & Waschulewski, M. Female preferences for naturally-occurring novel male traits. Behaviour 136, 519–527 (1999).Article 

Google Scholar 
Witte, K. & Klink, K. No pre-existing bias in sailfin molly females, Poecilia latipinna, for a sword in males. Behaviour 142, 283–303 (2005).Article 

Google Scholar 
Gerlai, R. Animated images in the analysis of zebrafish behavior. Curr. Zool. 63, 35–44 (2017).Article 

Google Scholar 
Ioannou, C. C., Guttal, V. & Couzin, I. D. Predatory fish select for coordinated collective motion in virtual prey. Science 337, 1212–1215 (2012).Article 
ADS 
CAS 

Google Scholar 
Little, A. C., Jones, B. C. & DeBruine, L. M. Preferences for variation in masculinity in real male faces change across the menstrual cycle: Women prefer more masculine faces when they are more fertile. Pers. Ind. Diff. 45, 478–482 (2008).Article 

Google Scholar 
Little, A. C., Jones, B. C. & DeBruine, L. M. Facial attractiveness: Evolutionary based research. Phil. Trans. R. Soc. B. 366, 1638–1659 (2011).Article 

Google Scholar 
Morrison, E. R., Clark, A. P., Tiddeman, B. P. & Penton-Voak, I. S. Manipulating shape cues in dynamic human faces: Sexual dimorphism is preferred in female but not male faces. Ethology 116, 1234–1243 (2010).Article 

Google Scholar 
Kacsoh, B. Z., Bozler, J., Ramaswami, M. & Bosco, G. Social communication of predator-induced changes in Drosophila behavior and germ line physiology. eLife. 4, e07423 (2015).Article 

Google Scholar 
Caruana, N. & Seymour, K. Objects that induce face pareidolia are prioritized by the visual system. Brit. J. Psychol. 113, 496–507 (2022).Article 

Google Scholar 
Agrawal, S., Safarik, S. & Dickinson, M. The relative roles of vision and chemosensation in mate recognition of Drosophila melanogaster. J. Exp. Biol. 217, 2796–2805 (2014).
Google Scholar 
R Development Core Team. R: A Language and Environment for Statistical Computing (Austria, Vienna, 2021).
Google Scholar 
Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

Google Scholar 
Fox, J. & Weisberg, S. An {R} Companion to Applied Regression 2nd edn. (Sage Publishing, London, 2001).
Google Scholar  More

FAO. Global forest resources assessment. www.fao.org/publications (2015).Finlayson, M. et al. A Report of the Millennium Ecosystem Assessment. (The Cropper Foundation, 2005).Lal, R., & Lorenz, K. In Recarbonization of the Biosphere: Ecosystems and the Global Carbon Cycle (eds Lal, R., Lorenz, K., Hüttl, R. F., Schneider, B. U. & von Braun, J.) Ch. 9 (Springer, 2012).Gilliam, F. S. Forest ecosystems of temperate climatic regions: from ancient use to climate change. N. Phytologist 212, 871–887 (2016).Article 

Google Scholar 
de Gouvenain, R. C. & Silander, J. A. Temperate forests in Reference Module in Life Sciences (Elsevier, 2017).Keith, S. A., Newton, A. C., Morecroft, M. D., Bealey, C. E. & Bullock, J. M. Taxonomic homogenization of woodland plant communities over 70 years. Proc. R. Soc. B: Biol. Sci. 276, 3539–3544 (2009).Article 

Google Scholar 
Rackham, O. Ancient woodlands: modern threats. N. Phytologist 180, 571–586 (2008).Article 

Google Scholar 
Bernhardt-Römermann, M. et al. Drivers of temporal changes in temperate forest plant diversity vary across spatial scales. Glob. Chang. Biol. 21, 3726–3737 (2015).Article 
ADS 

Google Scholar 
Waller, D. M. & Alverson, W. S. The white-tailed deer: a keystone herbivore. Wildl. Soc. Bull. 25, 217–226 (1997).
Google Scholar 
Ramirez, J. I. Uncovering the different scales in deer–forest interactions. Ecol. Evol. 11, 5017–5024 (2021).Article 

Google Scholar 
Rooney, T. P., Wiegmann, S. M., Rogers, D. A. & Waller, D. M. Biotic impoverishment and homogenization in unfragmented forest understory communities. Conserv. Biol. 18, 787–798 (2004).Stockton, S. A., Allombert, S., Gaston, A. J. & Martin, J. L. A natural experiment on the effects of high deer densities on the native flora of coastal temperate rain forests. Biol. Conserv 126, 118–128 (2005).Article 

Google Scholar 
Hegland, S. J., Lilleeng, M. S. & Moe, S. R. Old-growth forest floor richness increases with red deer herbivory intensity. Ecol. Manag. 310, 267–274 (2013).Article 

Google Scholar 
Simončič, T., Bončina, A., Jarni, K. & Klopčič, M. Assessment of the long-term impact of deer on understory vegetation in mixed temperate forests. J. Veg. Sci. 30, 108–120 (2019).Article 

Google Scholar 
Vild, O. et al. The paradox of long-term ungulate impact: increase of plant species richness in a temperate forest. Appl. Veg. Sci. 20, 282–292 (2017).Article 

Google Scholar 
Russell, F. L., Zippin, D. B. & Fowler, N. L. Effects of white-tailed deer (Odocoileus virginianus) on plants, plant populations and communities: a review. Am. Midl. Nat. 146, 1–26 (2001).Article 

Google Scholar 
Öllerer, K. et al. Beyond the obvious impact of domestic livestock grazing on temperate forest vegetation–A global review. Biol. Conserv. 237, 209–219 (2019).Article 

Google Scholar 
Borer, E. T. et al. Nutrients cause grassland biomass to outpace herbivory. Nat. Commun. 11, 1–8 (2020).Article 
ADS 

Google Scholar 
Kaarlejärvi, E., Eskelinen, A. & Olofsson, J. Herbivores rescue diversity in warming tundra by modulating trait-dependent species losses and gains. Nat. Commun. 8, 1–8 (2017).
Google Scholar 
Simkin, S. M. et al. Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States. Proc. Natl Acad. Sci. USA 113, 4086–4091 (2016).Article 
ADS 
CAS 

Google Scholar 
Bobbink, R. et al. Global assessment of nitrogen deposition effects on terrestrial plant diversity: A synthesis. Ecol. Appl. 20, 30–59 (2010).Article 
CAS 

Google Scholar 
Reinecke, J., Klemm, G. & Heinken, T. Vegetation change and homogenization of species composition in temperate nutrient deficient Scots pine forests after 45 yr. J. Veg. Sci. 25, 113–121 (2014).Article 

Google Scholar 
Speed, J. D. M., Austrheim, G., Kolstad, A. L. & Solberg, E. J. Long-term changes in northern large-herbivore communities reveal differential rewilding rates in space and time. PLoS ONE 14, e0217166 (2019).Article 
CAS 

Google Scholar 
Valente, A. M., Acevedo, P., Figueiredo, A. M., Fonseca, C. & Torres, R. T. Overabundant wild ungulate populations in Europe: management with consideration of socio-ecological consequences. Mamm. Rev. 50, 353–366 (2020).Article 

Google Scholar 
Linnell, J. D. C. et al. The challenges and opportunities of coexisting with wild ungulates in the human-dominated landscapes of Europe’s Anthropocene. Biol. Conserv. 244, 108500 (2020).Waller, D. M. The Herbaceous Layer in Forests of Eastern North America (ed. Gilliam, F.) Ch. 16 (Oxford Univ. Press, 2014).Kerley, G. I. H., Kowalczyk, R. & Cromsigt, J. P. G. M. Conservation implications of the refugee species concept and the European bison: king of the forest or refugee in a marginal habitat? Ecography 35, 519–529 (2011).Svenning, J. C. A review of natural vegetation openness in north-western Europe. Biol. Conserv 104, 133–148 (2002).Article 

Google Scholar 
Sandom, C. J., Ejrnaes, R., Hansen, M. D. D. & Svenning, J. C. High herbivore density associated with vegetation diversity in interglacial ecosystems. Proc. Natl Acad. Sci. USA 111, 4162–4167 (2014).Article 
ADS 
CAS 

Google Scholar 
Ramirez, J. I., Jansen, P. A., den Ouden, J., Goudzwaard, L. & Poorter, L. Long-term effects of wild ungulates on the structure, composition and succession of temperate forests. Ecol. Manag. 432, 478–488 (2019).Article 

Google Scholar 
Ramirez, J. I., Jansen, P. A. & Poorter, L. Effects of wild ungulates on the regeneration, structure and functioning of temperate forests: A semi-quantitative review. Ecol. Manag. 424, 406–419 (2018).Article 

Google Scholar 
Albert, A. et al. Seed dispersal by ungulates as an ecological filter: a trait-based meta-analysis. Oikos 124, 1109–1120 (2015).Article 

Google Scholar 
McNaughton, S. J. Grazing lawns: on domesticated and wild grazers. Am. Nat. 128, 937–939 (1986).Article 

Google Scholar 
Cromsigt, J. P. G. M. & Kuijper, D. P. J. Revisiting the browsing lawn concept: evolutionary Interactions or pruning herbivores? Perspect. Plant Ecol. 13, 207–215 (2011).Article 

Google Scholar 
Ramirez, J. I. et al. Temperate forests respond in a non-linear way to a population gradient of wild deer. Forestry 94, 502–511 (2021).Article 

Google Scholar 
Boulanger, V. et al. Ungulates increase forest plant species richness to the benefit of non‐forest specialists. Glob. Chang. Biol. 24, e485–e495 (2018).Article 

Google Scholar 
Kirby, K. J. The impact of deer on the ground flora of British broadleaved woodland. Forestry 74, 219–229 (2001).Article 

Google Scholar 
Royo, A. A., Collins, R., Adams, M. B., Kirschbaum, C. & Carson, W. P. Pervasive interactions between ungulate browsers and disturbance regimes promote temperate forest herbaceous diversity. Ecology 91, 93–105 (2010).Happonen, K. et al. Trait-based responses to land use and canopy dynamics modify long-term diversity changes in forest understories. Glob. Ecol. Biogeogr. 30, 1863–1875 (2021).Article 

Google Scholar 
Peñuelas, J. & Sardans, J. The global nitrogen-phosphorus imbalance. Science 375, 266–267 (2022).Article 
ADS 

Google Scholar 
Staude, I. R. et al. Replacements of small- by large-ranged species scale up to diversity loss in Europe’s temperate forest biome. Nat. Ecol. Evol. 4, 802–808 (2020).Article 

Google Scholar 
Newbold, T. et al. Widespread winners and narrow-ranged losers: Land use homogenizes biodiversity in local assemblages worldwide. PLoS Biol. 16, e2006841 (2018).Article 

Google Scholar 
Verheyen, K. et al. Driving factors behind the eutrophication signal in understorey plant communities of deciduous temperate forests. Br. Ecol. Soc. J. Ecol. 100, 352–365 (2012).
Google Scholar 
Gilliam, F. S. Response of the herbaceous layer of forest ecosystems to excess nitrogen deposition. J. Ecol. 94, 1176–1191 (2006).Article 
CAS 

Google Scholar 
de Schrijver, A. et al. Cumulative nitrogen input drives species loss in terrestrial ecosystems. Glob. Ecol. Biogeogr. 652, 803–816 (2011).Article 

Google Scholar 
de Frenne, P. et al. Light accelerates plant responses to warming. Nat. Plants 1, 15110 (2015).Article 

Google Scholar 
Baeten, L. et al. Herb layer changes (1954-2000) related to the conversion of coppice-with-standards forest and soil acidification. Appl. Veg. Sci. 12, 187–197 (2009).Article 

Google Scholar 
Becker, T., Spanka, J., Schröder, L. & Leuschner, C. Forty years of vegetation change in former coppice-with-standards woodlands as a result of management change and N deposition. Appl. Veg. Sci. 20, 304–313 (2017).Article 

Google Scholar 
van Calster, H. et al. Diverging effects of overstorey conversion scenarios on the understorey vegetation in a former coppice-with-standards forest. Ecol. Manag. 256, 519–528 (2008).Article 

Google Scholar 
Luyssaert, S. et al. The European carbon balance. Part 3: forests. Glob. Chang. Biol. 16, 1429–1450 (2010).Article 
ADS 

Google Scholar 
Kirby, K. J. et al. Five decades of ground flora changes in a temperate forest: the good, the bad and the ambiguous in biodiversity terms. Ecol. Manag. 505, 119896 (2022).Article 

Google Scholar 
Hautier, Y., Niklaus, P. A. & Hector, A. Competition for light causes plant biodiversity loss after eutrophication. Science 324, 636–638 (2009).Article 
ADS 
CAS 

Google Scholar 
Kowalczyk, R., Kamiński, T. & Borowik, T. Do large herbivores maintain open habitats in temperate forests? For. Ecol. Manag. 494, 119310 (2021).Dormann, C. F. et al. Plant species richness increases with light availability, but not variability, in temperate forests understorey. BMC Ecol. 20, 1–9 (2020).Article 

Google Scholar 
Dirnböck, T. et al. Forest floor vegetation response to nitrogen deposition in Europe. Glob. Chang. Biol. 20, 429–440 (2014).Article 
ADS 

Google Scholar 
Perring, M. P. et al. Understanding context dependency in the response of forest understorey plant communities to nitrogen deposition. Environ. Pollut. 242, 1787–1799 (2018).Article 
CAS 

Google Scholar 
Anderson, T. M. et al. Herbivory and eutrophication mediate grassland plant nutrient responses across a global climatic gradient. Ecology 99, 822–831 (2018).Article 

Google Scholar 
Gough, L. & Grace, J. B. Herbivore effects on plant species density at varying productivity levels. Ecology 79, 1586–1594 (1998).Article 

Google Scholar 
Eskelinen, A., Harpole, W. S., Jessen, M.-T., Virtanen, R. & Hautier, Y. Light competition drives herbivore and nutrient effects on plant diversity. Nature 611, 301–305 (2022).Knight, T. M., Dunn, J. L., Smith, L. A., Davis, J. A. & Kalisz, S. Deer facilitate invasive plant success in a Pennsylvania forest understory. Nat. Areas 29, 110–116 (2009).Article 

Google Scholar 
Beguin, J., Pothier, D. & Côté, S. D. Deer browsing and soil disturbance induce cascading effects on plant communities: a multilevel path analysis. Ecol. Appl. 21, 439–451 (2011).Gilliam, F. S. et al. Twenty-five-year response of the herbaceous layer of a temperate hardwood forest to elevated nitrogen deposition. Ecosphere 7, e01250 (2016).Article 

Google Scholar 
de Frenne, P. et al. Microclimate moderates plant responses to macroclimate warming. Proc. Natl Acad. Sci. USA 110, 18561–18565 (2013).Article 
ADS 

Google Scholar 
Hedwall, P. O. et al. Half a century of multiple anthropogenic stressors has altered northern forest understory plant communities. Ecol. Appl. 29, e01874 (2019).Perring, M. P. et al. Global environmental change effects on plant community composition trajectories depend upon management legacies. Glob. Chang. Biol. 24, 1722–1740 (2018).Article 
ADS 

Google Scholar 
Boulanger, V. et al. Decreasing deer browsing pressure influenced understory vegetation dynamics over 30 years. Ann. Sci. 72, 367–378 (2015).Article 

Google Scholar 
Bernes, C. et al. Manipulating ungulate herbivory in temperate and boreal forests: effects on vegetation and invertebrates. A systematic review. Environ. Evid. 7, 1–32 (2018).Article 

Google Scholar 
Reimoser, F. Steering the impacts of ungulates on temperate forests. J. Nat. Conserv. 10, 243–252 (2003).Article 

Google Scholar 
Vavra, M., Parks, C. G. & Wisdom, M. J. Biodiversity, exotic plant species, and herbivory: the good, the bad, and the ungulate. Ecol. Manag. 246, 66–72 (2007).Article 

Google Scholar 
Depauw, L. et al. Light availability and land-use history drive biodiversity and functional changes in forest herb layer communities. J. Ecol. 108, 1411–1425 (2020).Article 
CAS 

Google Scholar 
Chevaux, L. et al. Effects of stand structure and ungulates on understory vegetation in managed and unmanaged forests. Ecol. Appl. 32, e01874 (2022).Gordon, I. J. Browsing and grazing ruminants: are they different beasts? Ecol. Manag. 181, 13–21 (2003).Article 

Google Scholar 
Brasseur, B. et al. What deep‐soil profiles can teach us on deep‐time pH dynamics after land use change? Land Degrad. Dev. 29, 2951–2961 (2018).Article 

Google Scholar 
Schmitz, A. et al. Responses of forest ecosystems in Europe to decreasing nitrogen deposition. Environ. Pollut. 244, 980–994 (2019).Article 
CAS 

Google Scholar 
Dirnböck, T. et al. Currently legislated decreases in nitrogen deposition will yield only limited plant species recovery in European forests. Environ. Res. Lett. 13, 125010 (2018).Article 

Google Scholar 
Peterken, G. F. Natural Woodland: Ecology and Conservation in Northern Temperate Regions (Cambridge Univ. Press, 1996).Chamberlain, S. A. & Boettiger, C. R Python, and Ruby clients for GBIF species occurrence data. preprint. PeerJ Preprints 5, e3304v1 (2017).Chamberlain, S. A. & Szöcs, E. taxize: taxonomic search and retrieval in R. F1000Res 2, 191 (2013).Article 

Google Scholar 
Hédl, R., Kopecký, M. & Komárek, J. Half a century of succession in a temperate oakwood: from species-rich community to mesic forest. Divers Distrib. 16, 267–276 (2010).Article 

Google Scholar 
Giménez-Anaya, A., Herrero, J., Rosell, C., Couto, S. & García-Serrano, A. Food habits of wild boars (Sus scrofa) in a Mediterranean coastal wetland. Wetlands 28, 197–203 (2008).Article 

Google Scholar 
Barrios-Garcia, M. N. & Ballari, S. A. Impact of wild boar (Sus scrofa) in its introduced and native range: a review. Biol. Invasions 14, 2283–2300 (2012).Article 

Google Scholar 
Andersen, R. et al. An overview of the progress and challenges of peatland restoration in Western Europe. Restor. Ecol. 25, 271–282 (2017).Article 

Google Scholar 
Faurby, S. et al. PHYLACINE 1.2: the phylogenetic atlas of mammal macroecology. Ecology 99, 2626 (2018).Article 

Google Scholar 
van den Berg, L. J. L. et al. Evidence for differential effects of reduced and oxidised nitrogen deposition on vegetation independent of nitrogen load. Environ. Pollut. 208, 890–897 (2016).Article 

Google Scholar 
McNaughton, S. J., Oesterheld, M., Frank, D. A. & Williams, K. J. Ecosystem-level patterns of primary productivity and herbivory in terrestrial habitats. Nature 341, 142–144 (1989).Article 
ADS 
CAS 

Google Scholar 
Koerner, S. E. et al. Change in dominance determines herbivore effects on plant biodiversity. Nat. Ecol. Evol. 2, 1925–1932 (2018).Article 

Google Scholar 
Fréjaville, T. & Garzón, M. B. The EuMedClim database: yearly climate data (1901-2014) of 1 km resolution grids for Europe and the Mediterranean Basin. Front. Ecol. Evol. 6, 1–5 (2018).Article 

Google Scholar 
Al‐Yaari, A. et al. Asymmetric responses of ecosystem productivity to rainfall anomalies vary inversely with mean annual rainfall over the conterminous United States. Glob. Chang. Biol. 26, 6959–6973 (2020).Article 
ADS 

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

Google Scholar 
Hedges, L. V., Gurevitch, J. & Curtis, P. S. The meta-analysis of response ratios in experimental ecology. Spec. Feature Ecol. 80, 1150–1156 (1999).
Google Scholar 
Hillebrand, H. et al. Biodiversity change is uncoupled from species richness trends: consequences for conservation and monitoring. J. Appl. Ecol. 55, 169–184 (2018).Article 

Google Scholar 
Holz, H., Segar, J., Valdez, J. & Staude, I. R. Assessing extinction risk across the geographic ranges of plant species in Europe. Plants People Planet 4, 303–311 (2022).Article 

Google Scholar 
Staude, I. R. et al. Directional turnover towards larger‐ranged plants over time and across habitats. Ecol. Lett. 25, 466–482 (2021).Article 

Google Scholar 
Ellenberg, H., Weber, H. E., Düll, R., Wirth, V. & Werner, W. Zeigerwerte von Pflanzen in Mitteleuropa (Verlag Wrich Goltze, 2001).Chytrý, M., Tichý, L., Dřevojan, P., Sádlo, J. & Zelený, D. Ellenbergtype indicator values for the Czech flora. Preslia 90, 83–103 (2018).Bürkner, P.-C. brms: an R package for Bayesian multilevel models using Stan. J. Stat. Softw. 80, 1–28 (2017).Article 

Google Scholar 
Brooks, S. P. & Gelman, A. General methods for monitoring convergence of iterative simulations. J. Comput. Graph. Stat. 7, 434–455 (1998).MathSciNet 

Google Scholar 
Dushoff, J., Kain, M. P. & Bolker, B. M. I can see clearly now: reinterpreting statistical significance. Methods Ecol. Evol. 10, 756–759 (2019).Article 

Google Scholar 
Bradshaw, L. & Waller, D. M. Impacts of white-tailed deer on regional patterns of forest tree recruitment. Ecol. Manag. 375, 1–11 (2016).Article 

Google Scholar 
McGarvey, J. C., Bourg, N. A., Thompson, J. R., McShea, W. J. & Shen, X. Effects of twenty years of deer exclusion on woody vegetation at three life-history stages in a mid-atlantic temperate deciduous forest. Northeast. Nat. 20, 451–468 (2013).Nuttle, T., Ristau, T. E. & Royo, A. A. Long-term biological legacies of herbivore density in a landscape-scale experiment: forest understoreys reflect past deer density treatments for at least 20 years. J. Ecol. 102, 221–228 (2013). More

Cantwell-Jones, A. et al. Global plant diversity as a reservoir of micronutrients for humanity. Nat. Plants https://doi.org/10.1038/s41477-022-01100-6 (2022).Swenson, N. G. Phylogenetic imputation of plant functional trait databases. Ecography 37, 105–110 (2014).Article 

Google Scholar 
Swenson, N. G. et al. Phylogeny and the prediction of tree functional diversity across novel continental settings. Glob. Ecol. Biogeogr. 26, 553–562 (2017).Article 

Google Scholar 
Molina-Venegas, R. et al. Assessing among-lineage variability in phylogenetic imputation of functional trait datasets. Ecography 41, 1740–1749 (2018).Article 

Google Scholar 
Guénard, G., Legendre, P. & Peres-Neto, P. Phylogenetic eigenvector maps: a framework to model and predict species traits. Methods Ecol. Evol. 4, 1120–1131 (2013).Article 

Google Scholar 
Guénard, G., Ohe, P. C., von der, Walker, S. C., Lek, S. & Legendre, P. Using phylogenetic information and chemical properties to predict species tolerances to pesticides. Proc. R. Soc. B 281, 20133239 (2014).Article 

Google Scholar 
Ezekiel, M. Methods of Correlation Analysis (John Wiley and Sons, 1930).Johnson, T. F., Isaac, N. J. B., Paviolo, A. & González-Suárez, M. Handling missing values in trait data. Glob. Ecol. Biogeogr. 30, 51–62 (2021).Article 

Google Scholar 
Debastiani, V. J., Bastazini, V. A. G. & Pillar, V. D. Using phylogenetic information to impute missing functional trait values in ecological databases. Ecol. Inform. 63, 101315 (2021).Article 

Google Scholar 
Goolsby, E. W., Bruggeman, J. & Ané, C. Rphylopars: fast multivariate phylogenetic comparative methods for missing data and within-species variation. Methods Ecol. Evol. 8, 22–27 (2017).Article 

Google Scholar  More

Baker, A. C., Glynn, P. W. & Riegl, B. Climate change and coral reef bleaching: an ecological assessment of long-term impacts, recovery trends and future outlook. Estuar. Coast Shelf Sci. 80, 435–471 (2008).Article 

Google Scholar 
Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359, 80–83 (2018).Article 
CAS 

Google Scholar 
Normille, D. El Niño’s warmth devastating reefs worldwide. Science 352, 2015–2016 (2016).
Google Scholar 
Morikawa, M. K. & Palumbi, S. R. Using naturally occurring climate resilient corals to construct bleaching-resistant nurseries. Proc Natl Acad Sci USA 116, 10586–10591 (2019).Safaie, A. et al. High frequency temperature variability reduces the risk of coral bleaching. Nat. Commun. 9, 1671 (2018).Article 

Google Scholar 
Thomas, L. et al. Mechanisms of thermal tolerance in Reef-building corals across a fine-grained environmental mosaic: lessons from Ofu. Am. Samoa. Front Mar. Sci. 4, 434 (2018).Article 

Google Scholar 
Kenkel, C. D., Meyer, E. & Matz, M. V. Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments. Mol. Ecol. 22, 4322–4334 (2013).Article 
CAS 

Google Scholar 
Gomulkiewicz, R. & Holt, R. D. When does evolution by natural selection prevent extinction? Evolution 49, 201–207 (1995).
Google Scholar 
Bruno, J. F., Siddon, C. E., Witman, J. D., Colin, P. L. & Toscano, M. A. El Niño related coral bleaching in Palau, western Caroline Islands. Coral Reefs 20, 127–136 (2001).Article 

Google Scholar 
Golbuu, Y. et al. Palau’s coral reefs show differential habitat recovery following the 1998-bleaching event. Coral Reefs 26, 319–332 (2007).Article 

Google Scholar 
van Woesik, R. et al. Climate-change refugia in the sheltered bays of Palau: analogs of future reefs. Ecol. Evol. 2, 2474–2484 (2012).Article 

Google Scholar 
Barkley, H. C. & Cohen, A. L. Skeletal records of community-level bleaching in Porites corals from Palau. Coral Reefs 35, 1407–1417 (2016).Article 

Google Scholar 
Gouezo, M. et al. Drivers of recovery and reassembly of coral reef communities. Proc. R. Soc. B Biol. Sci. 286, 20182908 (2019).Shamberger, K. E. F. et al. Diverse coral communities in naturally acidified waters of a Western Pacific reef. Geophys. Res. Lett. 41, 499–504 (2014).Article 

Google Scholar 
Barkley, H. C. et al. Changes in coral reef communities across a natural gradient in seawater pH. Sci. Adv. 1, e1500328 (2015).Article 

Google Scholar 
Fabricius, K. E., Mieog, J. C., Colin, P. L., Idip, D. & van Oppen, M. J. H. Identity and diversity of coral endosymbionts (zooxanthellae) from three Palauan reefs with contrasting bleaching, temperature and shading histories. Mol. Ecol. 13, 2445–2458 (2004).Article 
CAS 

Google Scholar 
Anthony, K. R. N., Kline, D. I., Diaz-Pulido, G., Dove, S. & Hoegh-Guldberg, O. Ocean acidification causes bleaching and productivity loss in coral reef builders. Proc. Natl Acad. Sci. USA 105, 17442–17446 (2008).Article 
CAS 

Google Scholar 
Gibbin, E. M., Putnam, H. M., Gates, R. D., Nitschke, M. R. & Davy, S. K. Species-specific differences in thermal tolerance may define susceptibility to intracellular acidosis in reef corals. Mar. Biol. 162, 717–723 (2015).Article 
CAS 

Google Scholar 
Boulay, J. N., Hellberg, M. E., Cortés, J. & Baums, I. B. Unrecognized coral species diversity masks differences in functional ecology. Proc. R. Soc. B Biol. Sci. 281, 20131580 (2013).Baums, I. B., Boulay, J. N., Polato, N. R. & Hellberg, M. E. No gene flow across the Eastern Pacific Barrier in the reef-building coral Porites lobata. Mol. Ecol. 21, 5418–5433 (2012).Article 

Google Scholar 
Forsman, Z. H., Wellington, G. M., Fox, G. E. & Toonen, R. J. Clues to unraveling the coral species problem: Distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits. PeerJ 3, e751 (2015).Article 

Google Scholar 
Levas, S. J., Grottoli, A. G., Hughes, A., Osburn, C. L. & Matsui, Y. Physiological and biogeochemical traits of bleaching and recovery in the mounding species of coral Porites lobata: implications for resilience in mounding corals. PLoS ONE 8, e63267 (2013).Article 
CAS 

Google Scholar 
Linsley, B. K. et al. Coral carbon isotope sensitivity to growth rate and water depth with Paleo-sea level implications. Nat. Commun. 10, 1–9 (2019).
Google Scholar 
Peyrot-Clausade, M., Hutchings, P. & Richard, G. Temporal variations of macroborers in massive Porites lobata on Moorea, French Polynesia. Coral Reefs 11, 161–166 (1992).Article 

Google Scholar 
Nanami, A. & Nishihira, M. Microhabitat association and temporal stability in reef fish assemblages on massive Porites microatolls. Ichthyol. Res. 51, 165–171 (2004).Article 

Google Scholar 
Cantin, N. E. & Lough, J. M. Surviving coral bleaching events: porites growth anomalies on the Great Barrier Reef. PLoS ONE 9, e88720 (2014).Article 

Google Scholar 
Carilli, J. E., Norris, R. D., Black, B., Walsh, S. M. & Mcfield, M. Century-scale records of coral growth rates indicate that local stressors reduce coral thermal tolerance threshold. Glob. Chang Biol. 16, 1247–1257 (2010).Article 

Google Scholar 
Cantin, N. E., Cohen, A. L., Karnauskas, K. B., Tarrant, A. M. & McCorkle, D. C. Ocean warming slows coral growth in the central Red Sea. Science 329, 322–325 (2010).Article 
CAS 

Google Scholar 
Lough, J. M. & Cooper, T. F. New insights from coral growth band studies in an era of rapid environmental change. Earth Sci. Rev. 108, 170–184 (2011).Article 
CAS 

Google Scholar 
Mollica, N. R. N. et al. Skeletal records of bleaching reveal different thermal thresholds of Pacific coral reef assemblages. Coral Reefs 38, 743–757 (2019).Article 

Google Scholar 
Barkley, H. C. et al. Repeat bleaching of a central Pacific coral reef over the past six decades (1960–2016). Commun. Biol. 1, 177 (2018).DeCarlo, T. M. & Cohen, A. L. Dissepiments, density bands and signatures of thermal stress in Porites skeletons. Coral Reefs 36, 749–761 (2017).Article 

Google Scholar 
DeCarlo, T. M. et al. Acclimatization of massive reef-building corals to consecutive heatwaves. Proc. R. Soc. B 286, 20190235 (2019).DeCarlo, T. M. The past century of coral bleaching in the Saudi Arabian central Red Sea. PeerJ 8, e10200 (2020).Article 

Google Scholar 
Silverstein, R. N., Cunning, R. & Baker, A. C. Change in algal symbiont communities after bleaching, not prior heat exposure, increases heat tolerance of reef corals. Glob. Chang Biol. 21, 236–249 (2015).Article 

Google Scholar 
Fabricius, K. E. Effects of irradiance, flow, and colony pigmentation on the temperature microenvironment around corals: Implications for coral bleaching? Limnol. Oceanogr. 51, 30–37 (2006).Article 

Google Scholar 
Edmunds, P. J., Putnam, H. M. & Gates, R. D. Photophysiological consequences of vertical stratification of Symbiodinium in tissue of the coral Porites lutea. Biol. Bull. 223, 226–235 (2012).Article 
CAS 

Google Scholar 
Smith, L. W., Wirshing, H., Baker, A. C. & Birkeland, C. Environmental versus genetic influences on growth rates of the corals Pocillopora eydouxi and Porites lobata. Pac. Sci. 62, 57–69 (2008).Article 

Google Scholar 
Kenkel, C. D. & Bay, L. K. Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition. PeerJ 2018, e6047 (2018).Article 

Google Scholar 
Sunde, J., Yıldırım, Y., Tibblin, P. & Forsman, A. Comparing the performance of microsatellites and RADseq in population genetic studies: analysis of data for Pike (Esox lucius) and a synthesis of previous studies. Front. Genet. 11, 218 (2020).Article 

Google Scholar 
Barkley, H. C., Cohen, A. L., McCorkle, D. C. & Golbuu, Y. Mechanisms and thresholds for pH tolerance in Palau corals. J. Exp. Mar. Biol. Ecol. 489, 7–14 (2017).Article 
CAS 

Google Scholar 
Mollica, N. R. et al. Ocean acidification affects coral growth by reducing skeletal density. Proc. Natl Acad. Sci. USA 115, 1754–1759 (2018).Article 
CAS 

Google Scholar 
DeCarlo, T. M. et al. Coral macrobioerosion is accelerated by ocean acidification and nutrients. Geology 43, 7–10 (2014).Article 

Google Scholar 
Manzello, D. P. et al. Role of host genetics and heat-tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida Keys with ocean warming. Glob. Chang Biol. 25, 1016–1031 (2019).Article 

Google Scholar 
Rippe, J. P., Dixon, G., Fuller, Z. L., Liao, Y. & Matz, M. Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract. Mol. Ecol. 1–17 https://doi.org/10.1111/mec.15931 (2021).Schoepf, V. et al. Thermally variable, macrotidal Reef habitats promote rapid recovery from mass coral bleaching. Front. Mar. Sci. 7, 245 (2020).Article 

Google Scholar 
Dixon, G. B. et al. Genomic determinants of coral heat tolerance across latitudes. Science 348, 1460–1462 (2015).Article 
CAS 

Google Scholar 
Baums, I. B. et al. Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic. Ecol. Appl. 29, 1–23 (2019).Article 

Google Scholar 
Gosselin, L. A. & Qian, P.-Y. Juvenile mortality in benthic marine invertebrates. Mar. Ecol. Prog. Ser. 146, 265–282 (1997).Article 

Google Scholar 
Gouezo, M. et al. Modelled larval supply predicts coral population recovery potential following disturbance. Mar. Ecol. Prog. Ser. 661, 127–145 (2021).Golbuu, Y., Gouezo, M., Kurihara, H., Rehm, L. & Wolanski, E. Long-term isolation and local adaptation in Palau’s Nikko Bay help corals thrive in acidic waters. Coral Reefs 35, 909–918 (2016).Article 

Google Scholar 
Golbuu, Y. et al. Predicting coral recruitment in Palau’s complex reef archipelago. PLoS ONE 7, e50998 (2012).Article 
CAS 

Google Scholar 
Barshis, D. J., Birkeland, C., Toonen, R. J., Gates, R. D. & Stillman, J. H. High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coral Porites lobata (Dana, 1846). J. Exp. Biol. jeb.188581 https://doi.org/10.1242/jeb.188581 (2018).Shamberger, K. E. F., Lentz, S. J. & Cohen, A. L. Low and variable ecosystem calcification in a coral reef lagoon under natural acidification. Limnol. Oceanogr. https://doi.org/10.1002/lno.10662 (2017).Cacciapaglia, C. & van Woesik, R. Climate-change refugia: shading reef corals by turbidity. Glob. Chang Biol. 22, 1145–1154 (2016).Article 

Google Scholar 
Anthony, K. R. Enhanced energy status of corals on coastal, high-turbidity reefs. Mar. Ecol. Prog. Ser. 319, 111–116 (2006).Article 

Google Scholar 
Houlbrèque, F. & Ferrier-Pagès, C. Heterotrophy in tropical scleractinian corals. Biol. Rev. Camb. Philos. Soc. 84, 1–17 (2009).Article 

Google Scholar 
Aichelman, H. E. et al. Heterotrophy mitigates the response of the temperate coral Oculina arbuscula to temperature stress. Ecol. Evol. 6, 6758–6769 (2016).Article 

Google Scholar 
Gómez‐Corrales, M. & Prada, C. Cryptic lineages respond differently to coral bleaching. Mol. Ecol. 0, 1–9 (2020).
Google Scholar 
Fifer, J. E., Yasuda, N., Yamakita, T., Bove, C. B. & Davies, S. W. Genetic divergence and range expansion in a western North Pacific coral. Sci. Total Environ. 152423 https://doi.org/10.1016/J.SCITOTENV.2021.152423 (2021).Euclide, P. T. et al. Attack of the PCR clones: rates of clonality have little effect on RAD-seq genotype calls. Mol. Ecol. Resour. 20, 66–78 (2020).Article 
CAS 

Google Scholar 
Noonan, S. H. C., DiPerna, S., Hoogenboom, M. O. & Fabricius, K. E. Effects of variable daily light integrals and elevated CO2 on the adult and juvenile performance of two Acropora corals. Mar. Biol. 169, 1–15 (2022).Article 

Google Scholar 
Martins, C. P. P. et al. Growth response of reef-building corals to ocean acidification is mediated by interplay of taxon-specific physiological parameters. Front. Mar. Sci. 0, 879 (2022).
Google Scholar 
Bairos-Novak, K. R., Hoogenboom, M. O., van Oppen, M. J. H. & Connolly, S. R. Coral adaptation to climate change: meta-analysis reveals high heritability across multiple traits. Glob. Chang. Biol. 27, 5694–5710 (2021).Article 
CAS 

Google Scholar 
Kenkel, C. D., Setta, S. P. & Matz, M. V. Heritable differences in fitness-related traits among populations of the mustard hill coral, Porites astreoides. Heredity 115, 509–516 (2015).Article 
CAS 

Google Scholar 
Dziedzic, K. E., Elder, H., Tavalire, H. & Meyer, E. Heritable variation in bleaching responses and its functional genomic basis in reef-building corals (Orbicella faveolata). Mol. Ecol. 28, 2238–2253 (2019).Article 

Google Scholar 
Quigley, K. M., Bay, L. K. & Oppen, M. J. H. Genome‐wide SNP analysis reveals an increase in adaptive genetic variation through selective breeding of coral. Mol. Ecol. 2176–2188 https://doi.org/10.1111/mec.15482 (2020).Veron, J. E. N. Corals of the World (Australian Institute of Marine Science, 2000).Polato, N. R., Concepcion, G. T., Toonen, R. J. & Baums, I. B. Isolation by distance across the Hawaiian Archipelago in the reef-building coral Porites lobata. Mol. Ecol. 19, 4661–4677 (2010).Article 
CAS 

Google Scholar 
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. & Cresko, W. A. Stacks: an analysis tool set for population genomics. Mol. Ecol. 22, 3124–3140 (2013).Article 

Google Scholar 
Puritz, J. B., Hollenbeck, C. M. & Gold, J. R. dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ 2, e431 (2014).Article 

Google Scholar 
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).Article 
CAS 

Google Scholar 
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv (2013).Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. ArXiv (2012).Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).Article 
CAS 

Google Scholar 
Kopelman, N. M., Mayzel, J., Jakobsson, M. & Rosenberg, N. A. CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Mol. Ecol. Resour. 15, 1179–1191 (2015).Article 
CAS 

Google Scholar 
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).Article 
CAS 

Google Scholar 
Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620 (2005).Article 
CAS 

Google Scholar 
Puechmaille, S. J. The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem. Mol. Ecol. Resour. 16, 608–627 (2016).Article 

Google Scholar 
Jombart, T. & Ahmed, I. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071 (2011).Article 
CAS 

Google Scholar 
Goudet, J. Hierfstat, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes. 5, 184–186 (2005).Zeileis, A. & Grothendieck, G. zoo: S3 infrastructure for regular and irregular time series. J. Stat. Softw. 14, 1–27 (2005).Ryan, J. A. & Ulrich, J. M. xts: eXtensible Time Series. Package at https://cran.r-project.org/package=xts (2018).LaJeunesse, T. C. Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs. Mar. Biol. 141, 387–400 (2002).Article 

Google Scholar 
LaJeunesse, T. C. & Trench, R. K. Biogeography of two species of Symbiodinium (Freudenthal) inhabiting the intertidal sea anemone Anthopleura elegantissima (Brandt). Biol. Bull. 199, 126–134 (2000).Article 
CAS 

Google Scholar  More