Philippa Kaur

1.Jarau, S. & Hrncir, M. Food Exploitation by Social Insects: Ecological, Behavioral, and Theoretical Approaches. (CRC Press, 2009).2.Detrain, C. & Deneubourg, J.-L. Collective decision-making and foraging patterns in ants and honeybees. Adv. Insect Physiol. 35, 123–173 (2008) (Elsevier).
Google Scholar 
3.Hölldobler, B. & Wilson, E. O. The Ants (Harvard University Press, 1990).
Google Scholar 
4.Beckers, R., Deneubourg, J.-L. & Goss, S. Modulation of trail laying in the ant Lasius niger (Hymenoptera: Formicidae) and its role in the collective selection of a food source. J. Insect Behav. 6, 751–759 (1993).
Google Scholar 
5.Detrain, C. & Prieur, J. Sensitivity and feeding efficiency of the black garden ant Lasius niger to sugar resources. J. Insect Physiol. 64, 74–80 (2014).CAS 
PubMed 

Google Scholar 
6.Jackson, D. E. & Châline, N. Modulation of pheromone trail strength with food quality in Pharaoh’s ant, Monomorium pharaonic. Animal Behav. 74, 463–470 (2007).
Google Scholar 
7.Sumpter, D. J. T. & Beekman, M. From nonlinearity to optimality: Pheromone trail foraging by ants. Anim. Behav. 66, 273–280 (2003).
Google Scholar 
8.Cerdá, X., Angulo, E., Boulay, R. & Lenoir, A. Individual and collective foraging decisions: A field study of worker recruitment in the gypsy ant Aphaenogaster senilis. Behav. Ecol. Sociobiol. 63, 551–562 (2009).
Google Scholar 
9.Detrain, C. & Deneubourg, J.-L. Scavenging by Pheidole pallidula key for understanding decision-making systems in ants. Anim. Behav. 53, 537–547 (1997).
Google Scholar 
10.Mailleux, A.-C., Deneubourg, J. L. & Detrain, C. How do ants assess food volume?. Anim. Behav. 59, 1061–1069 (2000).CAS 
PubMed 

Google Scholar 
11.Breed, M. D., Fewell, J. H., Moore, A. J. & Williams, K. R. Graded recruitment in a ponerine ant. Behav. Ecol. Sociobiol. 20, 407–411 (1987).
Google Scholar 
12.Cammaerts, M.-C. & Cammaerts, R. Food recruitment strategies of the ants Myrmica sabuleti and Myrmica ruginodis. Behav. Proc. 5, 251–270 (1980).CAS 

Google Scholar 
13.Portha, S., Deneubourg, J.-L. & Detrain, C. Self-organized asymmetries in ant foraging: A functional response to food type and colony needs. Behav. Ecol. 13, 776–781 (2002).
Google Scholar 
14.Devigne, C. & Detrain, C. How does food distance influence foraging in the ant Lasius niger: The importance of home-range marking. Insect. Soc. 53, 46–55 (2006).
Google Scholar 
15.Fewell, J. H. Directional fidelity as a foraging constraint in the western harvester ant, Pogonomyrmex occidentalis. Oecologia 82, 45–51 (1990).ADS 
PubMed 

Google Scholar 
16.Howard, D. F. & Tschinkel, W. R. The effect of colony size and starvation on food flow in the fire ant, Solenopsis invicta (Hymenoptera: Formicidae). Behav. Ecol. Sociobiol. 7, 293–300 (1980).
Google Scholar 
17.Mailleux, A.-C., Devigne, C., Deneubourg, J.-L. & Detrain, C. Impact of starvation on Lasius niger’ exploration. Ethology 116, 248–256 (2010).
Google Scholar 
18.Portha, S., Deneubourg, J.-L. & Detrain, C. How food type and brood influence foraging decisions of Lasius niger scouts. Anim. Behav. 68, 115–122 (2004).
Google Scholar 
19.Deneubourg, J.-L., Goss, S., Pasteels, J. M. & Beckers, R. Collective decision making through food recruitment. Insectes Soc. 37, 258–267 (1990).
Google Scholar 
20.Czaczkes, T. J., Salmane, A. K., Klampfleuthner, F. A. M. & Heinze, J. Private information alone can trigger trapping of ant colonies in local feeding optima. J. Exp. Biol. 219, 744–751 (2016).PubMed 

Google Scholar 
21.Collett, T. S. & Collett, M. Memory use in insect visual navigation. Nat. Rev. Neurosci. 3, 542–552 (2002).CAS 
PubMed 
MATH 

Google Scholar 
22.Azevedo, D. L. O., Medeiros, J. C. & Araújo, A. Adjustments in the time, distance and direction of foraging in Dinoponera quadriceps Workers. J. Insect. Behav. 27, 177–191 (2014).
Google Scholar 
23.Beverly, B. D., McLendon, H., Nacu, S., Holmes, S. & Gordon, D. M. How site fidelity leads to individual differences in the foraging activity of harvester ants. Behav. Ecol. 20, 633–638 (2009).
Google Scholar 
24.Fourcassié, V. & Traniello, J. F. A. Food searching behaviour in the ant Formica schaufussi (Hymenoptera, Formicidae): Response of naive foragers to protein and carbohydrate food. Anim. Behav. 48, 69–79 (1994).
Google Scholar 
25.Aron, S., Beckers, R., Deneubourg, J. L. & Pasteels, J. M. Memory and chemical communication in the orientation of two mass-recruiting ant species. Ins. Soc. 40, 369–380 (1993).
Google Scholar 
26.Lehue, M., Detrain, C. & Collignon, B. Nest entrances, spatial fidelity, and foraging patterns in the red ant Myrmica rubra: A field and theoretical study. Insects 11, 317 (2020).PubMed Central 

Google Scholar 
27.Bolek, S., Wittlinger, M. & Wolf, H. What counts for ants? How return behaviour and food search of Cataglyphis ants are modified by variations in food quantity and experience. J. Exp. Biol. 215, 3218–3222 (2012).PubMed 

Google Scholar 
28.Detrain, C., Natan, C. & Deneubourg, J. L. The influence of the physical environment on the self-organised foraging patterns of ants. Naturwissenschaften 88, 171–174 (2001).ADS 
CAS 
PubMed 

Google Scholar 
29.Traniello, J. F. A., Fujita, M. S. & Bowen, R. V. Ant foraging behavior: Ambient temperature influences prey selection. Behav. Ecol. Sociobiol. 15, 65–68 (1984).
Google Scholar 
30.Nonacs, P. & Dill, L. M. Mortality risk versus food quality trade-offs in ants: Patch use over time. Ecol. Entomol. 16, 73–80 (1991).
Google Scholar 
31.Tanner, C. J. Individual experience-based foraging can generate community territorial structure for competing ant species. Behav. Ecol. Sociobiol. 63, 591–603 (2009).
Google Scholar 
32.Brown, M. J. F. & Gordon, D. M. How resources and encounters affect the distribution of foraging activity in a seed-harvesting ant. Behav. Ecol. Sociobiol. 47, 195–203 (2000).
Google Scholar 
33.Fourcassié, V., Schmitt, T. & Detrain, C. Impact of interference competition on exploration and food exploitation in the ant Lasius niger. Psyche J. Entomol. 2012, 1–8 (2012).
Google Scholar 
34.Mehdiabadi, N. & Gilbert, L. Colony-level impacts of parasitoid flies on fire ants. Proceedings of the Royal Society of London. Series B: Biological Sciences. 269, 1695–1699 (2002).35.Feener, D. H. Competition between ant species: Outcome controlled by parasitic flies. Science 214, 815–817 (1981).ADS 
PubMed 

Google Scholar 
36.Schmid-Hempel, P. Parasites in Social Insects (Princeton University Press, 1998).
Google Scholar 
37.Cremer, S., Armitage, S. A. O. & Schmid-Hempel, P. Social immunity. Curr. Biol. 17, 693–702 (2007).
Google Scholar 
38.Zhukovskaya, M., Yanagawa, A. & Forschler, B. Grooming behavior as a mechanism of insect disease defense. Insects 4, 609–630 (2013).PubMed 
PubMed Central 

Google Scholar 
39.Ortius-Lechner, D., Maile, R., Morgan, E. D. & Boomsma, J. J. Metapleural gland secretion of the leaf-cutter ant Acromyrmex octospinosus: New compounds and their functional significance. J. Chem. Ecol. 26, 1667–1683 (2000).CAS 

Google Scholar 
40.Ballari, S., Farji-Brener, A. G. & Tadey, M. Waste management in the leaf-cutting ant Acromyrmex lobicornis: Division of labour, aggressive behaviour, and location of external refuse dumps. J. Insect Behav. 20, 87–98 (2007).
Google Scholar 
41.Leclerc, J.-B. & Detrain, C. Impact of colony size on survival and sanitary strategies in fungus-infected ant colonies. Behav. Ecol. Sociobiol. 72, 1–10 (2018).42.Pereira, H., Jossart, M. & Detrain, C. Waste management by ants: The enhancing role of larvae. Anim. Behav. 168, 187–198 (2020).
Google Scholar 
43.Diez, L., Urbain, L., Lejeune, P. & Detrain, C. Emergency measures: Adaptive response to pathogen intrusion in the ant nest. Behav. Proc. 116, 80–86 (2015).
Google Scholar 
44.López-Riquelme, G. O. & Fanjul-Moles, M. L. The funeral ways of social insects. Social strategies for corpse disposal. Trends Entomol. 9, 71–129 (2013).45.Heinze, J. & Walter, B. Moribund ants leave their nests to die in social isolation. Curr. Biol. 20, 249–252 (2010).CAS 
PubMed 

Google Scholar 
46.Leclerc, J.-B. & Detrain, C. Loss of attraction for social cues leads to fungal-infected Myrmica rubra ants withdrawing from the nest. Anim. Behav. 129, 133–141 (2017).
Google Scholar 
47.Fouks, B. & Lattorff, H. M. G. Recognition and avoidance of contaminated flowers by foraging bumblebees (Bombus terrestris). PLoS ONE 6, e26328 (2011).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
48.Pereira, H. & Detrain, C. Pathogen avoidance and prey discrimination in ants. R. Soc. Open Sci. 7, 191705 (2020).ADS 
PubMed 
PubMed Central 

Google Scholar 
49.Pereira, H. & Detrain, C. Prophylactic avoidance of hazardous prey by the ant host Myrmica rubra. Insects 11, 444 (2020).PubMed Central 

Google Scholar 
50.Tranter, C., LeFevre, L., Evison, S. E. F. & Hughes, W. O. H. Threat detection: Contextual recognition and response to parasites by ants. ISBE 26, 396–405 (2015).
Google Scholar 
51.Marikovsky, P. I. On some features of behavior of the ants Formica rufa L. infected with fungous disease. Insectes Soc. 9, 173–179 (1962).
Google Scholar 
52.Lehue, M., Detrain, C. & Collignon, B. Nest entrances, spatial fidelity, and foraging patterns in the red ant Myrmica rubra: A field and theoretical study. Insects 11, 317 (2020).PubMed Central 

Google Scholar 
53.Diez, L., Deneubourg, J.-L., Hoebeke, L. & Detrain, C. Orientation in corpse-carrying ants: Memory or chemical cues?. Anim. Behav. 81, 1171–1176 (2011).
Google Scholar 
54.Brütsch, T., Felden, A., Reber, A. & Chapuisat, M. Ant queens (Hymenoptera: Formicidae) are attracted to fungal pathogens during the initial stage of colony founding. Myrmecol. News 20, 71–76 (2014).
Google Scholar 
55.Pontieri, L., Vojvodic, S., Graham, R., Pedersen, J. S. & Linksvayer, T. A. Ant colonies prefer infected over uninfected nest sites. PLoS ONE 9, e111961 (2014).ADS 
PubMed 
PubMed Central 

Google Scholar 
56.Leclerc, J.-B., Silva, J. P. & Detrain, C. Impact of soil contamination on the growth and shape of ant nests. R. Soc. Open Sci. 5, 180267 (2018).ADS 
PubMed 
PubMed Central 

Google Scholar 
57.Loreto, R. G. & Hughes, D. P. Disease dynamics in ants. Adv. Genet. 94, 287–306 (2016) (Elsevier).CAS 
PubMed 

Google Scholar 
58.Angelone, S. & Bidochka, M. J. Diversity and abundance of entomopathogenic fungi at ant colonies. J. Invertebr. Pathol. 156, 73–76 (2018).PubMed 

Google Scholar 
59.Evans, H. C., Groden, E. & Bischoff, J. F. New fungal pathogens of the red ant, Myrmica rubra, from the UK and implications for ant invasions in the USA. J. Funbiol. 114, 451–466 (2010).CAS 

Google Scholar 
60.Bos, N., Kankaanpää-Kukkonen, V., Freitak, D., Stucki, D. & Sundström, L. Comparison of twelve ant species and their susceptibility to fungal infection. Insects 10, 271 (2019).PubMed Central 

Google Scholar 
61.Theis, F. J., Ugelvig, L. V., Marr, C. & Cremer, S. Opposing effects of allogrooming on disease transmission in ant societies. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140108–20140108 (2015).
Google Scholar 
62.Okuno, M., Tsuji, K., Sato, H. & Fujisaki, K. Plasticity of grooming behavior against entomopathogenic fungus Metarhizium anisopliae in the ant Lasius japonicus. J. Ethol. 30, 23–27 (2012).
Google Scholar 
63.Pereira, R. M. & Stimac, J. L. Transmission of Beauveria bassiana within nests of Solenopsis invicta (Hymenoptera: Formicidae) in the laboratory. Environ. Entomol. 21, 1427–1432 (1992).
Google Scholar 
64.Hughes, W. O. H., Thomsen, L., Eilenberg, J. & Boomsma, J. J. Diversity of entomopathogenic fungi near leaf-cutting ant nests in a Neotropical forest, with particular reference to Metarhizium anisopliae var. anisopliae. J. Invertebr. Pathol. 85, 46–53 (2004).CAS 
PubMed 

Google Scholar 
65.Novak, S. & Cremer, S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. J. Theor. Biol. 372, 54–64 (2015).ADS 
MathSciNet 
PubMed 
MATH 

Google Scholar 
66.Qiu, H., Lu, L., Shi, Q. & He, Y. Fungus exposed Solenopsis invicta ants benefit from grooming. J. Insect. Behav. 27, 678–691 (2014).
Google Scholar 
67.Reber, A., Purcell, J., Buechel, S. D., Buri, P. & Chapuisat, M. The expression and impact of antifungal grooming in ants. J. Evol. Biol. 24, 954–964 (2011).CAS 
PubMed 

Google Scholar 
68.Sadd, B. M. & Schmid-Hempel, P. Insect immunity shows specificity in protection upon secondary pathogen exposure. Curr. Biol. 16, 1206–1210 (2006).CAS 
PubMed 

Google Scholar 
69.Traniello, J. F. A., Rosengaus, R. B. & Savoie, K. The development of immunity in a social insect: Evidence for the group facilitation of disease resistance. Proc. Natl. Acad. Sci. 99, 6838–6842 (2002).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
70.Konrad, M. et al. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biol. 10, e1001300 (2012).CAS 
PubMed 
PubMed Central 

Google Scholar 
71.Ugelvig, L. V. & Cremer, S. Social prophylaxis: Group interaction promotes collective immunity in ant colonies. Curr. Biol. 17, 1967–1971 (2007).CAS 
PubMed 

Google Scholar 
72.Bordoni, A. et al. No evidence of queen immunisation despite transgenerational immunisation in Crematogaster scutellaris ants. J. Insect Physiol. 120, 103998 (2020).CAS 
PubMed 

Google Scholar 
73.Reber, A. & Chapuisat, M. No evidence for immune priming in ants exposed to a fungal pathogen. PLoS ONE 7, e35372 (2012).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
74.Groden, E., Drummond, F. A., Garnas, J. & Franceour, A. Distribution of an invasive ant, Myrmica rubra (Hymenoptera: Formicidae), Maine. J. Econ. Entomol. 98, 1774–1784 (2005).PubMed 

Google Scholar 
75.Radchenko, A. & Elmes, G. W. Myrmica Ants (Hymenoptera: Formicidae) of the Old World (Natura optima dux Foundation, 2010).
Google Scholar 
76.Hänel, H. The life cycle of the insect pathogenic fungus Metarhizium anisopliae in the termite Nasutitermes exitiosus. Mycopathologia 80, 137–145 (1982).
Google Scholar 
77.Leclerc, J.-B. & Detrain, C. Ants detect but do not discriminate diseased workers within their nest. Sci. Nat. 103, 1–12 (2016).78.Lacey, L. A. Manual of Techniques in Invertebrate Pathology (Academic Press imprint of Elsevier Science, 2012).
Google Scholar 
79.R Core Team. R: A Language and Environment for Statistical Computing. (2020).80.Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2016).MATH 

Google Scholar 
81.Venables, W. N. & Ripley, B. D. Modern Applied Statistics with S (Springer, 2002).MATH 

Google Scholar 
82.Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using {lme4}. J. Stat. Softw. 67, 1–48 (2015).
Google Scholar 
83.Kuznetsova, A., Brockhoff, P. B. & Christensen, R. H. B. lmerTest package: Tests in linear mixed effects models. J. Stat. Soft. 82, 1–26. https://doi.org/10.18637/JSS.V082.I13 (2017).84.Lenth, R. Emmeans: Estimated marginal means, aka least-squares means. R-package version 1.4.8. https://CRAN.R-project.org/package=emmeans (2020).85.Hothorn, T., Bretz, F. & Westfall, P. Simultaneous inference in general parametric models. Biom. J. 50, 346–363 (2008).MathSciNet 
PubMed 
MATH 

Google Scholar 
86.Therneau, T. A Package for Survival Analysis in R. R-package version 3.2-3. https://CRAN.R-project.org/package=survival (2020) More

1.Melbourne, B. A. & Hastings, A. Highly variable spread rates in replicated biological invasions: Fundamental limits to predictability. Science 325, 1536–1539 (2009).ADS 
CAS 
PubMed 

Google Scholar 
2.Lewis, M. A., Petrovskii, S. V. & Potts, J. R. The Mathematics Behind Biological Invasions (Springer, 2016).MATH 

Google Scholar 
3.Phillips, B. L. Evolutionary processes make invasion speed difficult to predict. Biol. Invasions 17, 1949–1960 (2015).
Google Scholar 
4.Peischl, S., Kirkpatrick, M. & Excoffier, L. Expansion load and the evolutionary dynamics of a species range. Am. Nat. 185, E81–E93 (2015).PubMed 

Google Scholar 
5.Burton, O. J., Travis, J. M. J. & Phillips, B. L. Trade-offs and the evolution of life-histories during range expansion. Ecol. Lett. 13, 1210–1220 (2010).PubMed 

Google Scholar 
6.Phillips, B. L. & Perkins, T. A. Spatial sorting as the spatial analogue of natural selection. Theor. Ecol. 12, 155–163 (2019).
Google Scholar 
7.Deforet, M., Carmona-Fontaine, C., Korolev, K. S. & Xavier, J. B. Evolution at the edge of expanding populations. Am. Nat. 194, 291–305 (2019).PubMed 
PubMed Central 

Google Scholar 
8.Travis, J. M. J. & Dytham, C. Dispersal evolution during invasions. Evol. Ecol. Res. 4, 1119–1129 (2002).
Google Scholar 
9.Bouin, E. et al. Invasion fronts with variable motility: Phenotype selection, spatial sorting and wave acceleration. C. R. Math. 350, 761–766 (2012).MathSciNet 
MATH 

Google Scholar 
10.Shine, R., Brown, G. P. & Phillips, B. L. An evolutionary process that assembles phenotypes through space rather than through time. Proc. Natl. Acad. Sci. USA 108, 5708–5711 (2011).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
11.Williams, J. L., Kendall, B. E. & Levine, J. M. Rapid evolution accelerates plant population spread in fragmented experimental landscapes. Science 353, 482–485 (2016).ADS 
CAS 
PubMed 

Google Scholar 
12.Weiss-Lehman, C., Hufbauer, R. A. & Melbourne, B. A. Rapid trait evolution drives increased speed and variance in experimental range expansions. Nat. Commun. 8, 14303 (2017).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
13.Ochocki, B. M. & Miller, T. E. Rapid evolution of dispersal ability makes biological invasions faster and more variable. Nat. Commun. 8, 14315 (2017).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
14.Urban, M. C., Phillips, B. L., Skelly, D. K. & Shine, R. The cane toad’s (Chaunus [Bufo] marinus) increasing ability to invade Australia is revealed by a dynamically updated range model. Proc. R. Soc. B 274, 1413–1419 (2007).PubMed 
PubMed Central 

Google Scholar 
15.Phillips, B. L., Brown, G. P. & Shine, R. Evolutionarily accelerated invasions: The rate of dispersal evolves upwards during the range advance of cane toads. J. Evol. Biol. 23, 2595–2601 (2010).CAS 
PubMed 

Google Scholar 
16.Chuang, A. & Peterson, C. R. Expanding population edges: Theories, traits, and trade-offs. Glob. Change Biol. 22, 494–512 (2016).ADS 

Google Scholar 
17.Phillips, B. L., Brown, G. P., Travis, J. M. & Shine, R. Reid’s paradox revisited: The evolution of dispersal kernels during range expansion. Am. Nat. 172, S34–S48 (2008).PubMed 

Google Scholar 
18.Alford, R. A., Brown, G. P., Schwarzkopf, L., Phillips, B. L. & Shine, R. Comparisons through time and space suggest rapid evolution of dispersal behaviour in an invasive species. Wildl. Res. 36, 23–28 (2009).
Google Scholar 
19.Lindström, T., Brown, G. P., Sisson, S. A., Phillips, B. L. & Shine, R. Rapid shifts in dispersal behavior on an expanding range edge. Proc. Natl. Acad. Sci. USA 110, 13452–13456 (2013).ADS 
PubMed 
PubMed Central 

Google Scholar 
20.Brown, G. P., Phillips, B. L. & Shine, R. The straight and narrow path: The evolution of straight-line dispersal at a cane toad invasion front. Proc. R. Soc. B 281, 20141385 (2014).PubMed 
PubMed Central 

Google Scholar 
21.DeVore, J., Ducatez, S. & Shine, R. Spatial ecology of cane toads (Rhinella marina) in their native range: A study from French Guiana. Sci. Rep. 11, 11817 (2021).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
22.Brattstrom, B. H. Homing in the giant toad, Bufo marinus. Herpetologica 18, 176–180 (1962).
Google Scholar 
23.Zug, G. R. & Zug, P. B. The marine toad Bufo marinus: A natural history resumé of native populations. Smithson. Contrib. Zool. 284, 1–58 (1979).
Google Scholar 
24.Bayliss, P. The ecology of post-metamorphic Bufo marinus in central Amazonian savanna, Brazil. Unpublished Ph.D. thesis (The University of Queensland, 1995).25.Turvey, N. Cane Toads: A Tale of Sugar, Politics and Flawed Science (Sydney University Press, 2013).
Google Scholar 
26.Carpenter, C. C. & Gillingham, J. C. Water hole fidelity in the marine toad, Bufo marinus. J. Herpetol. 21, 158–161 (1987).
Google Scholar 
27.Ward-Fear, G., Greenlees, M. J. & Shine, R. Toads on lava: Spatial ecology and habitat use of invasive cane toads (Rhinella marina) in Hawai’i. PLoS ONE 11, e0151700 (2016).PubMed 
PubMed Central 

Google Scholar 
28.Hastings, A. Can spatial variation alone lead to selection for dispersal? Theor. Popul. Biol. 24, 244–251 (1983).MATH 

Google Scholar 
29.Möbius, W., et al. The collective effect of finite-sized inhomogeneities on the spatial spread of populations in two dimensions. Preprint at http://arxiv.org/abs/1910.05332 (2019).30.Urban, M. C., Phillips, B. L., Skelly, D. K. & Shine, R. A toad more traveled: The heterogeneous invasion dynamics of cane toads in Australia. Am. Nat. 171, E134–E148 (2008).PubMed 

Google Scholar 
31.Macgregor, L. F., Greenlees, M., de Bruyn, M. & Shine, R. An invasion in slow motion: The spread of invasive cane toads (Rhinella marina) into cooler climates in southern Australia. Biol. Invasions 23(11), 3565–3581 (2021).
Google Scholar 
32.Perkins, A. T., Phillips, B. L., Baskett, M. L. & Hastings, A. Evolution of dispersal and life history interact to drive accelerating spread of an invasive species. Ecol. Lett. 16, 1079–1087 (2013).PubMed 

Google Scholar 
33.Seabrook, W. Range expansion of the introduced cane toad Bufo marinus in New South Wales. Aust. Zool. 27, 58–62 (1991).
Google Scholar 
34.Kearney, M. R. et al. Modelling species distributions without using species distributions: The cane toad in Australia under current and future climates. Ecography 31, 423–434 (2008).
Google Scholar 
35.McCann, S. M., Kosmala, G. K., Greenlees, M. J. & Shine, R. Physiological plasticity in a successful invader: Rapid acclimation to cold occurs only in cool-climate populations of cane toads (Rhinella marina). Conserv. Physiol. 6, cox072 (2018).PubMed 
PubMed Central 

Google Scholar 
36.Schwarzkopf, L. & Alford, R. A. Nomadic movement in tropical toads. Oikos 96, 492–506 (2002).
Google Scholar 
37.Seebacher, F. & Alford, R. A. Movement and microhabitat use of a terrestrial amphibian (Bufo marinus) on a tropical island: Seasonal variation and environmental correlates. J. Herpetol. 33, 208–214 (1999).
Google Scholar 
38.Phillips, B. L., Brown, G. P., Greenlees, M., Webb, J. K. & Shine, R. Rapid expansion of the cane toad (Bufo marinus) invasion front in tropical Australia. Austral Ecol. 32, 169–176 (2007).
Google Scholar 
39.Tingley, R. & Shine, R. Desiccation risk drives the spatial ecology of an invasive anuran (Rhinella marina) in the Australian semi-desert. PLoS ONE 6, e25979 (2011).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
40.Brown, G. P., Phillips, B. L., Webb, J. K. & Shine, R. Toad on the road: Use of roads as dispersal corridors by cane toads (Bufo marinus) at an invasion front in tropical Australia. Biol. Conserv. 133, 88–94 (2006).
Google Scholar 
41.Pettit, L. J., Greenlees, M. J. & Shine, R. Is the enhanced dispersal rate seen at invasion fronts a behaviourally plastic response to encountering novel ecological conditions? Biol. Lett. 12, 20160539 (2016).PubMed 
PubMed Central 

Google Scholar 
42.Jessop, T. S. et al. Exploring mechanisms and origins of reduced dispersal in island Komodo Dragons. Proc. R. Soc. B 285, 20181829 (2018).PubMed 
PubMed Central 

Google Scholar 
43.Mayr, E. Animal Species and Evolution (Harvard University Press, 1963).
Google Scholar 
44.Duckworth, R. A. The role of behavior in evolution: A search for mechanism. Evol. Ecol. 23, 513–531 (2009).
Google Scholar 
45.Muñoz, M. M. & Losos, J. B. Thermoregulatory behavior simultaneously promotes and forestalls evolution in a tropical lizard. Am. Nat. 191, E15–E26 (2017).PubMed 

Google Scholar 
46.Carroll, S. P. et al. And the beak shall inherit–evolution in response to invasion. Ecol. Lett. 8, 944–951 (2005).PubMed 

Google Scholar 
47.Stuart, Y. E. et al. Rapid evolution of a native species following invasion by a congener. Science 346, 463–466 (2014).ADS 
CAS 
PubMed 

Google Scholar 
48.Acevedo, A. A., Lampo, M. & Cipriani, R. The cane or marine toad, Rhinella marina (Anura, Bufonidae): Two genetically and morphologically distinct species. Zootaxa 4103, 574–586 (2016).PubMed 

Google Scholar 
49.Reilly, S. M. et al. Conquering the world in leaps and bounds: Hopping locomotion in toads is actually bounding. Funct. Ecol. 29, 1308–1316 (2015).
Google Scholar 
50.Griffis-Kyle, K. L., Kyle, S. & Jungels, J. Use of breeding sites by arid-land toads in rangelands: Landscape-level factors. Southwest. Nat. 56, 251–255 (2011).
Google Scholar 
51.Sinsch, U. Movement ecology of amphibians: From individual migratory behaviour to spatially structured populations in heterogeneous landscapes. Can. J. Zool. 92, 491–502 (2014).
Google Scholar 
52.Cayuela, H. et al. Determinants and consequences of dispersal in vertebrates with complex life cycles: A review of pond-breeding amphibians. Q. Rev. Biol. 95, 1–36 (2020).
Google Scholar 
53.Child, T., Phillips, B. L., Brown, G. P. & Shine, R. The spatial ecology of cane toads (Bufo marinus) in tropical Australia: Why do metamorph toads stay near the water? Austral Ecol. 33, 630–640 (2008).
Google Scholar 
54.Pettit, L., Ducatez, S., DeVore, J. L., Ward-Fear, G. & Shine, R. Diurnal activity in cane toads (Rhinella marina) is geographically widespread. Sci. Rep. 10, 5723 (2020).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
55.Shine, R., Ward-Fear, G. & Brown, G. P. A famous failure: Why were cane toads an ineffective biocontrol in Australia? Conserv. Sci. Pract. 2, e296 (2020).
Google Scholar 
56.Shine, R., Everitt, C., Woods, D. & Pearson, D. J. An evaluation of methods used to cull invasive cane toads in tropical Australia. J. Pest Sci. 91, 1081–1091 (2018).
Google Scholar 
57.Silvester, R., Greenlees, M., Shine, R. & Oldroyd, B. Behavioural tactics used by invasive cane toads (Rhinella marina) to exploit apiaries in Australia. Austral Ecol. 44, 237–244 (2019).
Google Scholar 
58.Finnerty, P. B., Shine, R. & Brown, G. P. The costs of parasite infection: Effects of removing lungworms on performance, growth and survival of free-ranging cane toads. Funct. Ecol. 32, 402–415 (2018).
Google Scholar 
59.Pettit, L., Greenlees, M. & Shine, R. The impact of transportation and translocation on dispersal behaviour in the invasive cane toad. Oecologia 184, 411–422 (2017).ADS 
PubMed 

Google Scholar 
60.Kraus, F. Alien Reptiles and Amphibians: A Scientific Compendium and Analysis (Springer, 2008).
Google Scholar 
61.McCann, S., Greenlees, M. J. & Shine, R. On the fringe of the invasion: The ecological impact of cane toads in marginally suitable habitats. Biol. Invasions 19, 2729–2737 (2017).
Google Scholar 
62.S. Kaiser et al., unpubl. Data.63.Finnerty, P., Shine, R. & Brown, G. P. Survival of the faeces: Does a nematode lungworm adaptively manipulate the behaviour of its cane toad host? Ecol. Evol. 8, 4606–4618 (2018).PubMed 
PubMed Central 

Google Scholar 
64.Brown, G. P., Kelehear, C., Pizzatto, L. & Shine, R. The impact of lungworm parasites on rates of dispersal of their anuran host, the invasive cane toad. Biol. Invasions 18, 103–114 (2016).
Google Scholar 
65.G. Ward-Fear et al., unpubl. Data. More

1.Walther, G. et al. Ecological responses to recent climate change. Nature 416, 389–395 (2002).ADS 
CAS 
PubMed 

Google Scholar 
2.Intergovernmental Panel on Climate Change (IPCC). Climate Change 2014: Impacts, Adaptation, and Vulnerability Part A (Cambridge University Press, 2014).
Google Scholar 
3.Smith, V. H. Eutrophication of freshwater and coastal marine ecosystems. A global problem. Environ. Sci. Pollut. Res. 10, 126–139 (2003).CAS 

Google Scholar 
4.Cañedo-Argüelles, M., Kefford, B. & Schäfer, R. Salt in freshwaters: Causes, effects and prospects—introduction to the theme issue. Philos. Trans. R. Soc. B Biol. Sci. 374, 20 (2019).
Google Scholar 
5.Bernhardt, E. S., Rosi, E. J. & Gessner, M. O. Synthetic chemicals as agents of global change. Front. Ecol. Environ. 15, 84–90 (2017).
Google Scholar 
6.Hooper, D. U. et al. A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature 486, 105–108 (2012).ADS 
CAS 
PubMed 

Google Scholar 
7.Díaz, S. et al. Summary for policymakers of the global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. IPBES (2019).8.Parmesan, C. & Yohe, G. A globally coherent fingerprint of climate change impacts across natural systems. Nature 421, 37–42 (2003).ADS 
CAS 
PubMed 

Google Scholar 
9.Hoffmann, A. A. & Sgrò, C. M. Climate change and evolutionary adaptation. Nature 470, 479–485 (2011).ADS 
CAS 
PubMed 

Google Scholar 
10.DeWitt, T. J., Sih, A. & Wilson, D. S. Costs and limits of phenotypic plasticity. Trends Ecol. Evol. 13, 77–81 (1998).CAS 
PubMed 

Google Scholar 
11.Gienapp, P., Teplitsky, C., Alho, J. S., Mills, J. A. & Merilä, J. Climate change and evolution: Disentangling environmental and genetic responses. Mol. Ecol. 17, 167–178 (2008).CAS 
PubMed 

Google Scholar 
12.Fox, R. J., Donelson, J. M., Schunter, C., Ravasi, T. & Gaitán-Espitia, J. D. Beyond buying time: The role of plasticity in phenotypic adaptation to rapid environmental change. Philos. Trans. R. Soc. B Biol. Sci. 374, 20 (2019).
Google Scholar 
13.Salamin, N., Wüest, R. O., Lavergne, S., Thuiller, W. & Pearman, P. B. Assessing rapid evolution in a changing environment. Trends Ecol. Evol. 25, 692–698 (2010).PubMed 

Google Scholar 
14.Hairston, N. G., Ellner, S. P., Geber, M. A., Yoshida, T. & Fox, J. A. Rapid evolution and the convergence of ecological and evolutionary time. Ecol. Lett. 8, 1114–1127 (2005).
Google Scholar 
15.Govaert, L., Pantel, J. H. & De Meester, L. Eco-evolutionary partitioning metrics: Assessing the importance of ecological and evolutionary contributions to population and community change. Ecol. Lett. 19, 839–853 (2016).PubMed 

Google Scholar 
16.Diamond, S. E. & Martin, R. A. The interplay between plasticity and evolution in response to human-induced environmental change. F1000Research 5, 1–10 (2016).
Google Scholar 
17.Barraclough, T. G. How do species interactions affect evolutionary dynamics across whole communities?. Annu. Rev. Ecol. Evol. Syst. 46, 25–48 (2015).
Google Scholar 
18.De Meester, L. et al. Analysing eco-evolutionary dynamics—The challenging complexity of the real world. Funct. Ecol. 33, 43–59 (2019).
Google Scholar 
19.Kleynhans, E. J., Otto, S. P., Reich, P. B. & Vellend, M. Adaptation to elevated CO2 in different biodiversity contexts. Nat. Commun. 7, 20 (2016).
Google Scholar 
20.Walther, G. R. Community and ecosystem responses to recent climate change. Philos. Trans. R. Soc. B Biol. Sci. 365, 2019–2024 (2010).
Google Scholar 
21.Kooyers, N. J., James, B. & Blackman, B. K. Competition drives trait evolution and character displacement between Mimulus species along an environmental gradient. Evolution (N.Y.) 71, 1205–1221 (2017).CAS 

Google Scholar 
22.Lawrence, D. et al. Species interactions alter evolutionary responses to a novel environment. PLoS Biol. 10, 20 (2012).
Google Scholar 
23.terHorst, C. P., Lennon, J. T. & Lau, J. A. The relative importance of rapid evolution for plant-microbe interactions depends on ecological context. Proc. R. Soc. B Biol. Sci. 281, 20 (2014).
Google Scholar 
24.Lau, J. A., Shaw, R. G., Reich, P. B. & Tiffin, P. Indirect effects drive evolutionary responses to global change. New Phytol. 201, 335–343 (2014).CAS 
PubMed 

Google Scholar 
25.Yoshida, T., Jones, L. E., Ellner, S. P., Fussmann, G. F. & Hairston, N. G. Rapid evolution drives ecological dynamics in a predator–prey system. Nature 424, 303–306 (2003).ADS 
CAS 
PubMed 

Google Scholar 
26.Hart, S. P., Turcotte, M. M. & Levine, J. M. Effects of rapid evolution on species coexistence. Proc. Natl. Acad. Sci. 116, 2112–2117 (2019).CAS 
PubMed 
PubMed Central 

Google Scholar 
27.Grainger, T. N., Rudman, S. M., Schmidt, P. & Levine, J. M. Competitive history shapes rapid evolution in a seasonal climate. Proc. Natl. Acad. Sci. 118, e22015772118 (2021).
Google Scholar 
28.McGrady-Steed, J., Harris, P. M. & Morin, P. J. Biodiversity regulates ecosystem predictability. Nature 390, 162–165 (1997).ADS 
CAS 

Google Scholar 
29.Altermatt, F. et al. Big answers from small worlds: A user’s guide for protist microcosms as a model system in ecology and evolution. Methods Ecol. Evol. 6, 218–231 (2015).
Google Scholar 
30.Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl. Acad. Sci. USA 115, 6506–6511 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
31.Stoecker, D. & Pierson, J. Predation on protozoa: Its importance to zooplankton revisited. J. Plankton Res. 41, 367–373 (2019).
Google Scholar 
32.Berninger, U.-G., Finlay, B. J. & Kuuppo-Leinikki, P. Protozoan control of bacterial abundances in freshwater. Limnol. Oceanogr. 36, 139–147 (1991).ADS 

Google Scholar 
33.Williams, W. D. Anthropogenic salinisation of inland waters. Hydrobiologia 466, 329–337 (2001).
Google Scholar 
34.Herbert, E. R. et al. A global perspective on wetland salinization: Ecological consequences of a growing threat to freshwater wetlands. Ecosphere 6, 1–43 (2015).
Google Scholar 
35.Neubauer, S. C. & Craft, C. B. Global change and tidal freshwater wetlands: Scenarios and impacts. Tidal Freshw. Wetl. 20, 20 (2009).
Google Scholar 
36.Osmond, M. M. & de Mazancourt, C. How competition affects evolutionary rescue. Philos. Trans. R. Soc. B Biol. Sci. 368, 20 (2013).
Google Scholar 
37.terHorst, C. P. et al. Evolution in a community context: Trait responses to multiple species interactions. Am. Nat. 191, 368–380 (2018).
Google Scholar 
38.Donelson, J. M. et al. Understanding interactions between plasticity, adaptation and range shifts in response to marine environmental change. Philos. Trans. R. Soc. B Biol. Sci. 374, 20 (2019).
Google Scholar 
39.Vanvelk, H., Govaert, L., van den Berg, E. M., Brans, K. I. & De Meester, L. Interspecific differences, plastic, and evolutionary responses to a heat wave in three co-occurring Daphnia species. Limnol. Oceanogr. 20, 1–20. https://doi.org/10.1002/lno.11675 (2020).Article 

Google Scholar 
40.Svensson, F., Norberg, J. & Snoeijs, P. Diatom cell size, Coloniality and motility: Trade-Offs between temperature, Salinity and nutrient supply with climate change. PLoS One 9, 25 (2014).
Google Scholar 
41.Karp-Boss, L. & Boss, E. The elongated, the squat and the spherical: Selective pressures for phytoplankton shape. In Aquatic Microbial Ecology and Biogeochemistry: A Dual Perspective (eds Glibert, P. & Kana, T.) 25–34 (Springer, 2016).
Google Scholar 
42.Finley, H. E. Toleration of fresh water Protozoa to increased salinity. Ecology 11, 337–347 (1930).
Google Scholar 
43.Chen, H. & Jiang, J. G. Osmotic responses of Dunaliella to the changes of salinity. J. Cell. Physiol. 219, 251–258 (2009).CAS 
PubMed 

Google Scholar 
44.Shetty, P., Gitau, M. M. & Maróti, G. Salinity stress responses and adaptation mechanisms in eukaryotic green microalgae. Cells 8, 1–16 (2019).
Google Scholar 
45.terHorst, C. P. Evolution in response to direct and indirect ecological effects in pitcher plant inquiline communities. Am. Nat. 176, 675–685 (2010).PubMed 

Google Scholar 
46.Stoks, R., Govaert, L., Pauwels, K., Jansen, B. & De Meester, L. Resurrecting complexity: The interplay of plasticity and rapid evolution in the multiple trait response to strong changes in predation pressure in the water flea Daphnia magna. Ecol. Lett. 19, 180–190 (2016).PubMed 

Google Scholar 
47.Hendry, A. P. Key questions on the role of phenotypic plasticity in eco-evolutionary dynamics. J. Hered. 107, 25–41 (2016).PubMed 

Google Scholar 
48.Henn, J. J. et al. Intraspecific trait variation and phenotypic plasticity mediate alpine plant species response to climate change. Front. Plant Sci. 9, 1–11 (2018).ADS 

Google Scholar 
49.Johansson, J. Evolutionary responses to environmental changes:How does competition affect adaptation?. Evolution (N. Y.) 62, 421–435 (2008).
Google Scholar 
50.Li, S. J. et al. Microbial communities evolve faster in extreme environments. Sci. Rep. 4, 1–9 (2014).
Google Scholar 
51.Terhorst, C. P. Experimental evolution of protozoan traits in response to interspecific competition. J. Evol. Biol. 24, 36–46 (2011).CAS 
PubMed 

Google Scholar 
52.Carrara, F., Giometto, A., Seymour, M., Rinaldo, A. & Altermatt, F. Inferring species interactions in ecological communities: A comparison of methods at different levels of complexity. Methods Ecol. Evol. 6, 895–906 (2015).
Google Scholar 
53.Lorts, C. M. & Lasky, J. R. Competition × drought interactions change phenotypic plasticity and the direction of selection on Arabidopsis traits. New Phytol. 227, 1060–1072 (2020).CAS 
PubMed 

Google Scholar 
54.Hoffmann, A. A. & Hercus, M. J. Environmental stress as an evolutionary force. Bioscience 50, 217–226 (2000).
Google Scholar 
55.Klironomos, J. H. et al. Abrupt rise in atmospheric CO2 overestimates community response in a model plant-soil system. Nature 433, 621–624 (2005).ADS 
CAS 
PubMed 

Google Scholar 
56.Parmesan, C. Ecological and evolutionary responses to recent climate change. Annu. Rev. Ecol. Evol. Syst. 37, 637–669 (2006).
Google Scholar 
57.Finlay, B. J., Esteban, G. F., Olmo, J. L. & Tyler, P. A. Global distribution of free-living microbial species. Ecography (Cop.) 22, 138–144 (1999).
Google Scholar 
58.Fox, J. W. & McGrady-Steed, J. Stability and complexity in model ecosystems. J. Anim. Ecol. 71, 749–756 (2002).
Google Scholar 
59.Haddad, N. M. et al. Species’ traits predict the effects of disturbance and productivity on diversity. Ecol. Lett. 11, 348–356 (2008).PubMed 

Google Scholar 
60.Fronhofer, E. A. & Altermatt, F. Eco-evolutionary feedbacks during experimental range expansions. Nat. Commun. 6, 1–9 (2015).
Google Scholar 
61.Sonneborn, T. M. Chapter 12 methods in paramecium research. Methods Cell Biol. 4, 241–339 (1970).
Google Scholar 
62.Berger, H. & Foissner, W. Illustrated guide and ecological notes to ciliate species (Protozoa, Ciliophora) in running waters, lakes, and sewage plants. Handb. Angew. Limnol. Grundlagen-Gewässerbelastung-Restaurierung-Aquatische ökotoxikologie-Bewertung-Gewässerschutz 20, 1–60 (2014).
Google Scholar 
63.Cassidy-Hanley, D. M. Tetrahymena in the laboratory: Strain resources, methods for culture, maintenance, and storage. Methods Cell Biol. 109, 237–276 (2012).PubMed 
PubMed Central 

Google Scholar 
64.Sonzogni, W. C., Richardson, W., Rodgers, P. & Monteith, T. J. Chloride pollution of the Great Lakes. Water Pollut. Control Fed. 55, 513–521 (1983).CAS 

Google Scholar 
65.Lind, L. et al. Salty fertile lakes: How salinization and eutrophication alter the structure of freshwater communities. Ecosphere 9, 25 (2018).ADS 

Google Scholar 
66.Falconer, D. S. Introduction to Quantitative Genetics (Longman Group Ltd, 1981).
Google Scholar 
67.Pennekamp, F., Schtickzelle, N. & Petchey, O. L. BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes. Ecol. Evol. 5, 2584–2595 (2015).PubMed 
PubMed Central 

Google Scholar 
68.Pennekamp, F. et al. Dynamic species classification of microorganisms across time, abiotic and biotic environments—a sliding window approach. PLoS One 12, e0176682 (2017).PubMed 
PubMed Central 

Google Scholar 
69.Kuznetsova, A., Brockhoff, P. B., & Christensen, R. H. B. lmerTest: Tests for random and fixed effects for linear mixed effect models (lmer objects of lme4 package). R package version 2.0-6. Retrieved in July 7. (2014).70.Nakagawa, S. & Schielzeth, H. A general and simple method for obtaining R2 from generalized linear mixed-effects models. Methods Ecol. Evol. 4, 133–142 (2013).
Google Scholar 
71.Barton, K. MuMIn: Multi-Model Inference, Version 1.43.6. 1–75 (2019).72.Fronhofer, E. A., Gut, S. & Altermatt, F. Evolution of density-dependent movement during experimental range expansions. J. Evol. Biol. 30, 2165–2176 (2017).CAS 
PubMed 

Google Scholar 
73.Ellner, S. P., Geber, M. A. & Hairston, N. G. Does rapid evolution matter? Measuring the rate of contemporary evolution and its impacts on ecological dynamics. Ecol. Lett. 14, 603–614 (2011).PubMed 

Google Scholar 
74.Govaert, L. Eco-evolutionary partitioning metrics: A practical guide for biologists. Belgian J. Zool. 148, 167–202 (2018).
Google Scholar  More

1.Alvarez-Filip, L., Dulvy, N. K., Gill, J. A., Côté, I. M. & Watkinson, A. R. Flattening of Caribbean coral reefs: Region-wide declines in architectural complexity. Proc. R. Soc. B Biol. Sci. 276, 3019–3025 (2009).
Google Scholar 
2.Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).ADS 
CAS 
PubMed 

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

Google Scholar 
4.Halpern, B. S. et al. A global map of human impact on marine ecosystems. Science 319, 948–952 (2008).ADS 
CAS 
PubMed 

Google Scholar 
5.Loya, Y. et al. Coral bleaching: The winners and the losers. Ecol. Lett. 4, 122–131 (2001).
Google Scholar 
6.Anthony, K. R. N., Hoogenboom, M. O., Maynard, J. A., Grottoli, A. G. & Middlebrook, R. Energetics approach to predicting mortality risk from environmental stress: A case study of coral bleaching. Funct. Ecol. 23, 539–550 (2009).
Google Scholar 
7.Depczynski, M. et al. Bleaching, coral mortality and subsequent survivorship on a West Australian fringing reef. Coral Reefs 32, 233–238 (2013).ADS 

Google Scholar 
8.Edmunds, P. J. Implications of high rates of sexual recruitment in driving rapid reef recovery in Mo’orea, French Polynesia. Sci. Rep. 8, 16615. https://doi.org/10.1038/s41598-018-34686-z (2018).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
9.Richmond, R. H., Tisthammer, K. H. & Spies, N. P. The effects of anthropogenic stressors on reproduction and recruitment of corals and reef organisms. Front. Mar. Sci. 5, 266. https://doi.org/10.3389/fmars.2018.00226 (2018).Article 

Google Scholar 
10.Oliver, E. C. J. et al. Marine heatwaves. Ann. Rev. Mar. Sci. 13, 313–342 (2021).PubMed 

Google Scholar 
11.Rinkevich, B. The contribution of photosynthetic products to coral reproduction. Mar. Biol. 101, 259–263 (1989).CAS 

Google Scholar 
12.Lesser, M. P. Using energetic budgets to assess the effects of environmental stress on corals: Are we measuring the right things?. Coral Reefs 32, 25–33 (2013).ADS 

Google Scholar 
13.Muscatine, L., McCloskey, L. & Marian, R. Estimating the daily contribution of carbon from zooxanthellae to coral animal respiration. Limnol. Oceanogr. 26, 601–611 (1981).ADS 
CAS 

Google Scholar 
14.Rodrigues, L. J. & Grottoli, A. G. Energy reserves and metabolism as indicators of coral recovery from bleaching. Limnol. Oceanogr. 52, 1874–1882 (2007).ADS 

Google Scholar 
15.Rädecker, N. et al. Heat stress destabilizes symbiotic nutrient cycling in corals. Proc. Natl. Acad. Sci. USA 118, e2022653118. https://doi.org/10.1073/pnas.2022653118 (2021).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
16.Grottoli, A. G., Rodrigues, L. J. & Palardy, J. E. Heterotrophic plasticity and resilience in bleached corals. Nature 440, 1186–1189 (2006).ADS 
CAS 
PubMed 

Google Scholar 
17.Schoepf, V. et al. Annual coral bleaching and the long-term recovery capacity of coral. Proc. R. Soc. B 282, 20151887. https://doi.org/10.1098/rspb.2015.1997 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
18.Leuzinger, S., Willis, B. L. & Anthony, K. R. N. Energy allocation in a reef coral under varying resource availability. Mar. Biol. 159, 177–186 (2012).
Google Scholar 
19.Oren, U., Benayahu, Y., Lubinevsky, H. & Loya, Y. Colony integration during regeneration in the stony coral Favia favus. Ecology 82, 802–813 (2001).
Google Scholar 
20.Fisch, J., Drury, C., Towle, E. K., Winter, R. N. & Miller, M. W. Physiological and reproductive repercussions of consecutive summer bleaching events of the threatened Caribbean coral Orbicella faveolata. Coral Reefs 38, 863–876 (2019).ADS 

Google Scholar 
21.Ward, S., Harrison, P. & Hoegh-Guldberg, O. Coral bleaching reduces reproduction of scleractinian corals and increases susceptibility to future stress. Proc. 9th Int. Coral Reef Symp. 1123–1128 (2002).22.Levitan, D. R., Boudreau, W., Jara, J. & Knowlton, N. Long-term reduced spawning in Orbicella coral species due to temperature stress. Mar. Ecol. Prog. Ser. 515, 1–10 (2014).ADS 

Google Scholar 
23.Johnston, E. C., Counsell, C. W. W., Sale, T. L., Burgess, S. C. & Toonen, R. J. The legacy of stress: Coral bleaching impacts reproduction years later. Funct. Ecol. 34, 2315–2325 (2020).
Google Scholar 
24.Szmant, A. M. & Gassman, N. J. The effects of prolonged ‘bleaching’ on the tissue biomass and reproduction of the reef coral Montastrea annularis. Coral Reefs 8, 217–224 (1990).ADS 

Google Scholar 
25.Jones, A. M. & Berkelmans, R. Tradeoffs to thermal acclimation: energetics and reproduction of a reef coral with heat tolerant Symbiodinium Type-D. J. Mar. Biol. 2011, 185890. https://doi.org/10.1155/2011/185890 (2011).Article 

Google Scholar 
26.Figueiredo, J. et al. Ontogenetic change in the lipid and fatty acid composition of scleractinian coral larvae. Coral Reefs 31, 613–619 (2012).ADS 

Google Scholar 
27.Hagedorn, M. et al. Potential bleaching effects on coral reproduction. Reprod. Fertil. Dev. 28, 1061–1071 (2016).CAS 

Google Scholar 
28.Michalek-Wagner, K. & Willis, B. L. Impacts of bleaching on the soft coral Lobophytum compactum. I. Fecundity, fertilization and offspring viability. Coral Reefs 19, 231–239 (2001).
Google Scholar 
29.Howells, E. J. et al. Species-specific trends in the reproductive output of corals across environmental gradients and bleaching histories. Mar. Pollut. Bull. 105, 532–539 (2016).CAS 
PubMed 

Google Scholar 
30.Godoy, L. et al. Southwestern Atlantic reef-building corals Mussismilia spp. are able to spawn while fully bleached. Mar. Biol. 168, 15. https://doi.org/10.1007/s00227-021-03824-z (2021).CAS 
Article 

Google Scholar 
31.Veron, J. E. Acropora hyacinthus. in Corals of the World, vol. 1–3. (ed. Veron, J. E.) 404–405 (Australian Institute of Marine Sciences, 2000).32.Pratchett, M. S., McCowan, D., Maynard, J. A. & Heron, S. F. Changes in bleaching susceptibility among corals subject to ocean warming and recurrent bleaching in Moorea, French polynesia. PLoS ONE 8, e70443. https://doi.org/10.1371/journal.pone.0070443 (2013).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
33.Speare, K. E., Adam, T. C., Winslow, E. M., Lenihan, H. S. & Burkepile, D. E. Size-dependent mortality of corals during marine heatwave erodes recovery capacity of a coral reef. Glob. Change Biol. https://doi.org/10.1111/gcb.16000 (2021). Article 

Google Scholar 
34.Holbrook, S. J. et al. Recruitment drives spatial variation in recovery rates of resilient coral reefs. Sci. Rep. 8, 7338. https://doi.org/10.1038/s41598-018-25414-8 (2018).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
35.Carroll, A., Harrison, P. & Adjeroud, M. Sexual reproduction of Acropora reef corals at Moorea, French polynesia. Coral Reefs 25, 93–97 (2006).ADS 

Google Scholar 
36.Tsounis, G. et al. Anthropogenic effects on reproductive effort and allocation of energy reserves in the Mediterranean octocoral Paramuricea clavata. Mar. Ecol. Prog. Ser. 449, 161–172 (2012).ADS 

Google Scholar 
37.Wall, C. B., Ritson-Williams, R., Popp, B. N. & Gates, R. D. Spatial variation in the biochemical and isotopic composition of corals during bleaching and recovery. Limnol. Oceanogr. 64, 2011–2028 (2019).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
38.Jung, E. M. U., Stat, M., Thomas, L., Koziol, A. & Schoepf, V. Coral host physiology and symbiont dynamics associated with differential recovery from mass bleaching in an extreme, macro-tidal reef environment in northwest Australia. Coral Reefs 40, 893–905 (2021).
Google Scholar 
39.Tremblay, P., Gori, A., Maguer, J. F., Hoogenboom, M. & Ferrier-Pagès, C. Heterotrophy promotes the re-establishment of photosynthate translocation in a symbiotic coral after heat stress. Sci. Rep. 6, 38112. https://doi.org/10.1038/srep38112 (2016).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
40.Baumann, J., Grottoli, A. G., Hughes, A. D. & Matsui, Y. Photoautotrophic and heterotrophic carbon in bleached and non-bleached coral lipid acquisition and storage. J. Exp. Mar. Bio. Ecol. 461, 469–478 (2014).CAS 

Google Scholar 
41.Grottoli, A. G. et al. The cumulative impact of annual coral bleaching can turn some coral species winners into losers. Glob. Chang. Biol. 20, 3823–3833 (2014).ADS 
PubMed 

Google Scholar 
42.Graham, E. M., Baird, A. H., Connolly, S. R., Sewell, M. A. & Willis, B. L. Rapid declines in metabolism explain extended coral larval longevity. Coral Reefs 32, 539–549 (2013).ADS 

Google Scholar 
43.Michalek-Wagner, K. & Willis, B. L. Impacts of bleaching on the soft coral Lobophytum compactum. II. Biochemical changes in adults and their eggs. Coral Reefs 19, 240–246 (2001).
Google Scholar 
44.Harii, S., Nadaoka, K., Yamamoto, M. & Iwao, K. Temporal changes in settlement, lipid content and lipid composition of larvae of the spawning hermatypic coral Acropora tenuis. Mar. Ecol. Prog. Ser. 346, 89–96 (2007).ADS 
CAS 

Google Scholar 
45.Wallace, C. C. Reproduction, recruitment and fragmentation in nine sympatric species of the coral genus Acropora. Mar. Biol. 88, 217–233 (1985).
Google Scholar 
46.Ziegler, R. & Ibrahim, M. M. Formation of lipid reserves in fat body and eggs of the yellow fever mosquito, Aedes aegypti. J. Insect Physiol. 47, 623–627 (2001).CAS 
PubMed 

Google Scholar 
47.Baliña, S., Temperoni, B., Greco, L. S. L. & Tropea, C. Losing reproduction: effect of high temperature on female biochemical composition and egg quality in a freshwater crustacean with direct development, the red cherry shrimp, Neocaridina davidi (Decapoda, Atyidae). Biol. Bull. 234, 139–151 (2018).PubMed 

Google Scholar 
48.Levitan, D. R. The relationship between egg size and fertilization success in broadcast-spawning marine invertebrates. Integr. Comp. Biol. 46, 298–311 (2006).PubMed 

Google Scholar 
49.Caballes, C. F., Pratchett, M. S., Kerr, A. M. & Rivera-Posada, J. A. The role of maternal nutrition on oocyte size and quality, with respect to early larval development in the coral-eating starfish, Acanthaster planci. PLoS ONE 11, e0158007. https://doi.org/10.1371/journal.pone.0158007 (2016).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
50.Madin, J. S. et al. The Coral Trait Database, a curated database of trait information for coral species from the global oceans. Sci. Data 4, 160017. https://doi.org/10.1038/sdata.2016.17 (2017).Article 

Google Scholar 
51.Foster, T. & Gilmour, J. Egg size and fecundity of biannually spawning corals at Scott Reef. Sci. Rep. 10, 12313. https://doi.org/10.1038/s41598-020-68289-4 (2020).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
52.Harriott, V. J. Reproductive ecology of four scleratinian species at Lizard Island, Great Barrier Reef. Coral Reefs 2, 9–18 (1983).ADS 

Google Scholar 
53.Vargas-Ángel, B., Colley, S. B., Hoke, S. M. & Thomas, J. D. The reproductive seasonality and gametogenic cycle of Acropora cervicornis off Broward County, Florida, USA. Coral Reefs 25, 110–122 (2006).ADS 

Google Scholar 
54.Hall, V. R. & Hughes, T. P. Reproductive strategies of modular organisms: comparative studies of reef-building corals. Ecology 77, 950–963 (1996).
Google Scholar 
55.Brandt, M. E. The effect of species and colony size on the bleaching response of reef-building corals in the Florida Keys during the 2005 mass bleaching event. Coral Reefs 28, 911–924 (2009).ADS 

Google Scholar 
56.Sakai, K., Singh, T. & Iguchi, A. Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016. PeerJ 2019, e8138. https://doi.org/10.7717/peerj.8138 (2019).Article 

Google Scholar 
57.Nozawa, Y. & Lin, C. H. Effects of colony size and polyp position on polyp fecundity in the scleractinian coral genus Acropora. Coral Reefs 33, 1057–1066 (2014).ADS 

Google Scholar 
58.Álvarez-Noriega, M. et al. Fecundity and the demographic strategies of coral morphologies. Ecology 97, 3485–3493 (2016).PubMed 

Google Scholar 
59.Bena, C. & Van Woesik, R. The impact of two bleaching events on the survival of small coral colonies (Okinawa, Japan). Bull. Mar. Sci. 75, 115–125 (2004).
Google Scholar 
60.Shenkar, N., Fine, M. & Loya, Y. Size matters: Bleaching dynamics of the coral Oculina patagonica. Mar. Ecol. Prog. Ser. 294, 181–188 (2005).ADS 

Google Scholar 
61.Hughes, T. P. et al. Global warming impairs stock–recruitment dynamics of corals. Nature 568, 387–390 (2019).ADS 
CAS 
PubMed 

Google Scholar 
62.McClanahan, T. R., Maina, J., Moothien-Pillay, R. & Baker, A. C. Effects of geography, taxa, water flow, and temperature variation on coral bleaching intensity in Mauritius. Mar. Ecol. Prog. Ser. 298, 131–142 (2005).ADS 

Google Scholar 
63.Hoogenboom, M. O. et al. Environmental drivers of variation in bleaching severity of Acropora species during an extreme thermal anomaly. Front. Mar. Sci. 4, 376. https://doi.org/10.3389/fmars.2017.00376 (2017).Article 

Google Scholar 
64.Schoepf, V. et al. Thermally variable, macrotidal reef habitats promote rapid recovery from mass coral bleaching. Front. Mar. Sci. 7, 245. https://doi.org/10.3389/fmars.2020.00245 (2020).Article 

Google Scholar 
65.Golbuu, Y. et al. Palau’s coral reefs show differential habitat recovery following the 1998-bleaching event. Coral Reefs 26, 319–332 (2007).
Google Scholar 
66.van Woesik, R. et al. Climate-change refugia in the sheltered bays of Palau: Analogs of future reefs. Ecol. Evol. 2, 2474–2484 (2012).PubMed 
PubMed Central 

Google Scholar 
67.Penin, L., Adjeroud, M., Schrimm, M. & Lenihan, H. S. High spatial variability in coral bleaching around Moorea (French Polynesia): Patterns across locations and water depths. C. R. Biol. 330, 171–181 (2007).PubMed 

Google Scholar 
68.Penin, L., Vidal-Dupiol, J. & Adjeroud, M. Response of coral assemblages to thermal stress: Are bleaching intensity and spatial patterns consistent between events?. Environ. Monit. Assess. 185, 5031–5042 (2013).PubMed 

Google Scholar 
69.Brown, B. E., Downs, C. A., Dunne, R. P. & Gibb, S. W. Exploring the basis of thermotolerance in the reef coral Goniastrea aspera. Mar. Ecol. Prog. Ser. 242, 119–129 (2002).ADS 

Google Scholar 
70.Kenkel, C. D. et al. Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments. Mol. Ecol. 22, 4335–4348 (2013).CAS 
PubMed 

Google Scholar 
71.Burt, J. A. & Bauman, A. G. Suppressed coral settlement following mass bleaching in the southern Persian/Arabian Gulf. Aquat. Ecosyst. Heal. Manag. 23, 166–174 (2020).
Google Scholar 
72.Shlesinger, T. & Loya, Y. Breakdown in spawning synchrony: A silent threat to coral persistence. Science 365, 1002–1007 (2019).ADS 
CAS 
PubMed 

Google Scholar 
73.Edmunds, P., Gates, R. & Gleason, D. The biology of larvae from the reef coral Porites astreoides, and their response to temperature disturbances. Mar. Biol. 139, 981–989 (2001).
Google Scholar 
74.Edmunds, P. J. Spatiotemporal variation in coral recruitment and its association with seawater temperature. Limnol. Oceanogr. 66, 1394–1408 (2021).ADS 

Google Scholar 
75.Bouwmeester, J. et al. Latitudinal variation in monthly-scale reproductive synchrony among Acropora coral assemblages in the Indo-Pacific. Coral Reefs 40, 1411–1418 (2021).
Google Scholar 
76.Edmunds, P. J. MCR LTER: Coral reef: Long-term population and community dynamics: Corals, ongoing since 2005. knb-lter-mcr.4.38. 10.6073/pasta/10ee808a046cb63c0b8e3bc3c9799806 (2020).77.Claar, D. C. & Baum, J. K. Timing matters: Survey timing during extended heat stress can influence perceptions of coral susceptibility to bleaching. Coral Reefs 38, 559–565 (2019).ADS 

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

Google Scholar 
79.Leichter, J., Seydel, K. & Gotschalk, C. MCR LTER: Coral reef: Benthic water temperature, ongoing since 2005. knb-lter-mcr.1035.13. 10.6073/pasta/2087a33cdd16986352bed443fecc7fd7 (2020).80.Bradford, M. A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248–254 (1976).CAS 
PubMed 

Google Scholar 
81.Dubois, M., Gilles, K. A., Hamilton, J. K., Rebers, P. A. & Smith, F. Colorimetric method for determination of sugars and related substances. Anal. Chem. 28, 350–356 (1955).
Google Scholar 
82.Masuko, T. et al. Carbohydrate analysis by a phenol-sulfuric acid method in microplate format. Anal. Biochem. 339, 69–72 (2005).CAS 
PubMed 

Google Scholar 
83.Stimson, J. & Kinzie, R. A. The temporal pattern and rate of release of zooxanthellae from the reef coral Pocillopora damicornis (Linnaeus) under nitrogen-enrichment and control conditions. J. Exp. Mar. Bio. Ecol. 153, 63–74 (1991).
Google Scholar 
84.Szmant-Froelich, A., Rhetter, M. & Riggs, L. Sexual reproduction of Favis fragum (ESPER): lunar patterns of gametogenesis, embryogenesis and planulation in Puerto Rico. Bull. Mar. Sci. 37, 880–892 (1985).
Google Scholar  More

1.Amaja, L. G., Feyssa, D. H. & Gutema, T. M. Assessment of types of damage and causes of Human–wildlife conflict in Gera district, southwestern Ethiopia. J. Ecol. Nat. Environ. 8, 49–54 (2016).Article 

Google Scholar 
2.Decker, D. J., Laube, T. B. & Siemer, W. F. Human–Wildlife Conflict Management: A Practitioner’s Guide (Northeastern Wildlife Damage Management Research and Outreach Cooperative, 2002).
Google Scholar 
3.Habib, A., Nazir, I., Fazili, M. F. & Bhat, B. A. Human–wildlife conflict-causes, consequences and mitigation measures with special reference to Kashmir. J. Zool. Stud. 2, 26–30 (2015).
Google Scholar 
4.Eklund, A., Lopez-Bao, J. V., Tourani, M., Chapron, G. & Frank, J. Author Correction: Limited evidence on the effectiveness of interventions to reduce livestock predation by large carnivores. Sci. Rep. 8, 5770 (2018).ADS 
Article 

Google Scholar 
5.Hussain, S. The status of the snow leopard in Pakistan and its conflict with local farmers. Oryx 37, 26–33 (2003).Article 

Google Scholar 
6.Miller, J. R., Jhala, Y. V. & Schmitz, O. J. Human perceptions mirror realities of carnivore attack risk for livestock: Implications for mitigating human-carnivore conflict. PLoS ONE 11, e0162685 (2016).Article 

Google Scholar 
7.Aryal, P. et al. Human–carnivore conflict: Ecological and economical sustainability of predation on livestock by snow leopard and other carnivores in the Himalaya. Sustain. Sci. 9, 321–329 (2014).Article 

Google Scholar 
8.Khan, B. et al. Pastoralist experience and tolerance of snow leopard, wolf and lynx predation in Karakoram Pamir Mountains. J. Biol. Environ. Sci. 5, 214–229 (2014).
Google Scholar 
9.Jackson, R. M., Ahlborn, G., Gurung, M. & Ale, S. Reducing livestock depredation losses in the Nepalese Himalaya. In Proc. 17th Vertebrate Pest Conference (eds Timm, R. M. & Crabb, A. C.) 241–247 (University of California, 1996).
Google Scholar 
10.Qamar, Q. Z. et al. Human leopard conflict: An emerging issue of common leopard conservation in Machiara National Park, Azad Jammu, and Kashmir, Pakistan. Pak. J. Wildl. 1, 50–56 (2010).
Google Scholar 
11.Atickem, A., Williams, S., Bekele, A. & Thirgood, S. Livestock predation in the Bale Mountains, Ethiopia. Afr. J. Ecol. 48, 1076–1082 (2010).Article 

Google Scholar 
12.Gittleman, J. L., Funk, S. M., Macdonald, D. W. & Wayne, R. K. Carnivore conservation. Cambridge University Press, Cambridge consequences and mitigation measures with special reference to Kashmir. J. Zool. Stud. 2, 26–30 (2001).
Google Scholar 
13.Treves, A. K. & Karanth, K. U. Human–carnivore conflict—Local solutions with global applications (Special section): Introduction. Conserv. Biol. 17, 1489–1490 (2003).Article 

Google Scholar 
14.Li, J., Yin, H., Wang, D., Jiagong, Z. & Lu, Z. Human-snow leopard conflicts in the Sanjiangyuan Region of the Tibetan Plateau. Biol. Conserv. 166, 118–123 (2013).Article 

Google Scholar 
15.McCarthy, T. M. & Chapron, G. Snow Leopard Survival Strategy (IT and SLN, 2003).
Google Scholar 
16.Suryawanshi, K.R. Human carnivore conflicts: Understanding predation ecology and livestock damage by snow leopards. Ph.D. Thesis. Manipal University, India (2013).17.Bocci, A., Lovari, S., Khan, M. Z. & Mori, E. Sympatric snow leopards and Tibetan wolves: coexistence of large carnivores with human-driven potential competition. Eur. J. Wildl. Res. 63, 92 (2017).Article 

Google Scholar 
18.Wang, S. W. & Macdonald, D. Livestock predation by carnivores in Jigme Singye Wangchuck National Park, Bhutan. Biol. Conserv. 129, 558–565 (2006).Article 

Google Scholar 
19.Khan, M. Z., Khan, B., Awan, M. S. & Begum, F. Livestock depredation by large predators and its implications for conservation and livelihoods in the Karakoram Mountains of Pakistan. Oryx 52, 519–525 (2018).Article 

Google Scholar 
20.Ali, H., Younus, M., Din, J. U., Bischof, R. & Nawaz, M. A. Do Marco Polo argali Ovis ammon polii persist in Pakistan?. Oryx 53, 329–333 (2019).Article 

Google Scholar 
21.Dar, N. I., Minhas, R. A., Zaman, Q. & Linkie, M. Predicting the patterns, perceptions, and causes of human-carnivore conflict in and around Machiara National Park, Pakistan. Biol. Conserv. 142, 2076 (2009).Article 

Google Scholar 
22.RC Team. R: A Language and Environment for Statistical Computing (2013).23.Din, J. U. et al. A Tran’s boundary study of spatiotemporal patterns of livestock predation and prey preferences by snow leopard and wolf in the Pamir. Glob. Ecol. Conserv. 20, e00719 (2019).Article 

Google Scholar 
24.Conover, M. R. Resolving Human–Wildlife Conflicts: The Science of Wildlife Damage Management 418 (Lewis Publishers, 2002).
Google Scholar 
25.Graham, K., Beckerman, A. P. & Thirgood, S. Human–predator–prey conflicts: Ecological correlates, prey losses and patterns of management. Biol. Conserv. 122, 159–171 (2005).Article 

Google Scholar 
26.Li, X., Buzzard, P., Chen, Y. & Jiang, X. Patterns of livestock predation by carnivores: Human–wildlife conflict in Northwest Yunnan, China. Environ. Manage. 52, 1334–1340 (2013).ADS 
Article 

Google Scholar 
27.Dar, N. I., Minhas, R. A., Zaman, Q. & Linkie, M. Predicting the patterns, perceptions and causes of human–carnivore conflict in and around Machiara National Park, Pakistan. Biol. Conserv. 142, 2076–2082 (2009).Article 

Google Scholar 
28.Mishra, C., Prins, H. H. T. & van Wieren, S. E. Overstocking in the trans-Himalayan rangelands of India. Environ. Conserv. 28, 279–283 (1997).Article 

Google Scholar 
29.Hayward, M. W. & Kerley, G. I. H. Prey preferences of the lion (Panthera Leo). J. Zool. (Lond.) 267(267), 309–322 (2005).Article 

Google Scholar 
30.Mc Guinness, S. & Taylor, D. Farmers’ perceptions and actions to decrease crop raiding by forest-dwelling primates around a Rwandan Forest fragment. Hum. Dimens. Wildl. 19, 361–372 (2014).Article 

Google Scholar 
31.ICIMOD. Glacial Lakes and Glacial Lake Outburst Floods in Nepal (Gland, 2011).Book 

Google Scholar 
32.Distefano, E. Human–Wildlife Conflict Worldwide: Collection of Case Studies, Analysis of Management Strategies and Good Practices (Food and Agricultural Organization of the United Nations (FAO), 2005).
Google Scholar 
33.Shedayi, A. A., Xu, M., Naseer, I. & Khan, B. Altitudinal gradients of soil and vegetation carbon and nitrogen in a high altitude nature reserve of Karakoram ranges. Springerplus 5, 1–14 (2016).CAS 
Article 

Google Scholar  More

PatientsStool samples from a total of 52 patients with varying stages of CKD were collected in this study: CKD3A (n = 12), CKD3B (n = 11), CKD4 (n = 15), CKD5 (n = 4) and ESRD (n = 10) (Table 1). Patients’ characteristics are summarized in Table 1. Among 52 patients, 31 were reported to have Type 2 diabetes mellitus and 7 patients were reported to have human immunodeficiency virus (HIV) infection. As expected, urine protein creatinine ratio, serum creatinine and blood urea nitrogen level increased with progressing stages of CKD (CKD 3A to ESRD). There was no significant difference in fat, protein, carbohydrates, dietary fiber and calorie intake between CKD patients with different stages (Supplementary Table S1).Table 1 Patients’ characteristics.Full size tableAlpha and beta-diversityRichness and Shannon index were not significantly different between different patient groups, meanwhile the CKD5 group showed a significant decrease in Simpson diversity compared with CKD 3A (FDR  More

1.Flemming HC, Wuertz S. Bacteria and archaea on Earth and their abundance in biofilms. Nat Rev Microbiol. 2019;17:247–60.CAS 
PubMed 

Google Scholar 
2.Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 2012;337:1661–5.CAS 
PubMed 

Google Scholar 
3.Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31:533–8.CAS 
PubMed 

Google Scholar 
4.Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:1–11.
Google Scholar 
5.Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2:1533–42.CAS 
PubMed 

Google Scholar 
6.Gleeson T, Befus KM, Jasechko S, Luijendijk E, Cardenas MB. The global volume and distribution of modern groundwater. Nat Geosci. 2016;9:161–7.CAS 

Google Scholar 
7.Akob DM, Küsel K. Where microorganisms meet rocks in the Earth’s Critical Zone. Biogeosciences. 2011;8:3531–43.CAS 

Google Scholar 
8.Griebler C, Lueders T. Microbial biodiversity in groundwater ecosystems. Freshw Biol. 2009;54:649–77.
Google Scholar 
9.Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong WL, et al. Active sulfur cycling in the terrestrial deep subsurface. ISME J. 2020;14:1260–72.CAS 
PubMed 
PubMed Central 

Google Scholar 
10.Einsiedl F, Mayer B. Hydrodynamic and microbial processes controlling nitrate in a fissured-porous karst aquifer of the Franconian Alb, Southern Germany. Environ Sci Technol. 2006;40:6697–702.CAS 
PubMed 

Google Scholar 
11.Schlesinger WH. On the fate of anthropogenic nitrogen. Proc Natl Acad Sci USA. 2009;106:203–8.CAS 
PubMed 

Google Scholar 
12.McCollom TM, Seewald JS. Serpentinites, hydrogen, and life. Elements. 2013;9:129–34.CAS 

Google Scholar 
13.Emerson JB, Thomas BC, Alvarez W, Banfield JF. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environ Microbiol. 2016;18:1686–703.CAS 
PubMed 

Google Scholar 
14.Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, et al. Differential depth distribution of microbial function and putative symbionts through sediment- hosted aquifers in the deep terrestrial subsurface. Nat Microbiol. 2018;3:328–36.CAS 
PubMed 
PubMed Central 

Google Scholar 
15.Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, et al. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J. 2018;12:1715–28.CAS 
PubMed 
PubMed Central 

Google Scholar 
16.Wegner CE, Gaspar M, Geesink P, Herrmann M, Marz M, Küsel K. Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of the elements nitrogen, sulfur, and carbon. Appl Environ Microbiol. 2019;85:1–18.
Google Scholar 
17.Herrmann M, Rusznyak A, Akob DM, Schulze I, Opitz S, Totsche KU, et al. Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl Environ Microbiol. 2015;81:2384–94.CAS 
PubMed 
PubMed Central 

Google Scholar 
18.Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, et al. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. Environ Microbiol. 2017;19:459–74.CAS 
PubMed 

Google Scholar 
19.Jewell TNM, Karaoz U, Brodie EL, Williams KH, Beller HR. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer. ISME J. 2016;10:2106–17.CAS 
PubMed 
PubMed Central 

Google Scholar 
20.Handley KM, Bartels D, O’Loughlin EJ, Williams KH, Trimble WL, Skinner K, et al. The complete genome sequence for putative H2- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environ Microbiol. 2014;16:3443–62.CAS 
PubMed 

Google Scholar 
21.Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, et al. DNA stable-isotope probing. Nat Protoc. 2007;2:860–6.CAS 
PubMed 

Google Scholar 
22.von Bergen M, Jehmlich N, Taubert M, Vogt C, Bastida F, Herbst FA, et al. Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology. ISME J. 2013;7:1877–85.
Google Scholar 
23.Taubert M, Vogt C, Wubet T, Kleinsteuber S, Tarkka MT, Harms H, et al. Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium. ISME J. 2012;6:2291–301.CAS 
PubMed 
PubMed Central 

Google Scholar 
24.Taubert M, Baumann S, von Bergen M, Seifert J. Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP). Anal Bioanal Chem. 2011;401:1975–82.CAS 
PubMed 

Google Scholar 
25.Rimstidt JD, Vaughan DJ. Pyrite oxidation: a state-of-the-art assessment of the reaction mechanism. Geochim Cosmochim Acta. 2003;67:873–80.CAS 

Google Scholar 
26.Schippers A, Jozsa PG, Sand W. Sulfur chemistry in bacterial leaching of pyrite. Appl Environ Microbiol. 1996;62:3424–31.CAS 
PubMed 
PubMed Central 

Google Scholar 
27.Kohlhepp B, Lehmann R, Seeber P, Küsel K, Trumbore SE, Totsche KU. Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate-siliciclastic alternations of the Hainich CZE, central Germany. Hydrol Earth Syst Sci. 2017;21:6091–116.CAS 

Google Scholar 
28.Grimm F, Franz B, Dahl C. Thiosulfate and sulfur oxidation in purple sulfur bacteria. In: Dahl C, Friedrich CG, editors. Microbial Sulfur Metabolism. Berlin, Heidelberg: Springer; 2008. p. 101–16.29.Ghosh W, Dam B. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse Bacteria and Archaea. FEMS Microbiol Rev. 2009;33:999–1043.CAS 
PubMed 

Google Scholar 
30.Kumar S, Herrmann M, Blohm A, Hilke I, Frosch T, Trumbore SE, et al. Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiol Ecol. 2018;94:fiy141.CAS 

Google Scholar 
31.R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Core Team; 2019 [cited 2021]; Available from: https://www.R-project.org/.32.Ryabchykov O, Bocklitz T, Ramoji A, Neugebauer U, Foerster M, Kroegel C, et al. Automatization of spike correction in Raman spectra of biological samples. Chemom Intell Lab. 2016;155:1–6.CAS 

Google Scholar 
33.Dörfer T, Bocklitz T, Tarcea N, Schmitt M, Popp J. Checking and improving calibration of Raman spectra using chemometric approaches. Z Phys Chem. 2011;225:753–64.
Google Scholar 
34.Bocklitz TW, Dörfer T, Heinke R, Schmitt M, Popp J. Spectrometer calibration protocol for Raman spectra recorded with different excitation wavelengths. Spectrochim Acta A. 2015;149:544–9.CAS 

Google Scholar 
35.Guo SX, Heinke R, Stöckel S, Rösch P, Bocklitz T, Popp J. Towards an improvement of model transferability for Raman spectroscopy in biological applications. Vib Spectrosc. 2017;91:111–8.CAS 

Google Scholar 
36.Liland KH, Almoy T, Mevik BH. Optimal choice of baseline correction for multivariate calibration of spectra. Appl Spectrosc. 2010;64:1007–16.CAS 
PubMed 

Google Scholar 
37.Taubert M, Stöckel S, Geesink P, Girnus S, Jehmlich N, von Bergen M, et al. Tracking active groundwater microbes with D2O labelling to understand their ecosystem function. Environ Microbiol. 2018;20:369–84.CAS 
PubMed 

Google Scholar 
38.Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.CAS 

Google Scholar 
39.Seifert J, Taubert M, Jehmlich N, Schmidt F, Völker U, Vogt C, et al. Protein-based stable isotope probing (protein-SIP) in functional metaproteomics. Mass Spectrom Rev. 2012;31:683–97.CAS 
PubMed 

Google Scholar 
40.Taubert M. SIsCA. 2020 [updated 23.10.2020; cited 2021]; Available from: https://github.com/m-taubert/SIsCA.41.MacCoss MJ, Wu CC, Matthews DE, Yates JR. Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides. Anal Chem. 2005;77:7646–53.CAS 
PubMed 

Google Scholar 
42.Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.
Google Scholar 
43.Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J. Oxidation of reduced inorganic sulfur compounds by bacteria: Emergence of a common mechanism? Appl Environ Microbiol. 2001;67:2873–82.CAS 
PubMed 
PubMed Central 

Google Scholar 
44.Kelly DP, Shergill JK, Lu WP, Wood AP. Oxidative metabolism of inorganic sulfur compounds by bacteria. Antonie Van Leeuwenhoek. 1997;71:95–107.CAS 
PubMed 

Google Scholar 
45.Beller HR, Letain TE, Chakicherla A, Kane SR, Legler TC, Coleman MA. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic versus denitrifying conditions. J Bacteriol. 2006;188:7005–15.CAS 
PubMed 
PubMed Central 

Google Scholar 
46.Beller HR, Chain PSG, Letain TE, Chakicherla A, Larimer FW, Richardson PM, et al. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitfificans. J Bacteriol. 2006;188:1473–88.CAS 
PubMed 
PubMed Central 

Google Scholar 
47.McKinlay JB, Harwood CS. Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria. Proc Natl Acad Sci USA. 2010;107:11669–75.CAS 
PubMed 
PubMed Central 

Google Scholar 
48.Tabita FR. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a different perspective. Photosyn Res. 1999;60:1–28.CAS 

Google Scholar 
49.Berg IA. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol. 2011;77:1925–36.CAS 
PubMed 
PubMed Central 

Google Scholar 
50.Overholt WA, Trumbore S, Xu X, Bornemann TL, Probst AJ, Krüger M, et al. Rates of primary production in groundwater rival those in oligotrophic marine systems. bioRxiv 2021 [Preprint]. 2021. Available from: https://doi.org/10.1101/2021.10.13.464073.51.Alfreider A, Vogt C, Geiger-Kaiser M, Psenner R. Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes. Syst Appl Microbiol. 2009;32:140–50.CAS 
PubMed 

Google Scholar 
52.Herrmann M, Geesink P, Yan L, Lehmann R, Totsche KU, Küsel K. Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater. Water Res. 2020;170:115306.CAS 
PubMed 

Google Scholar 
53.Yan LJ, Herrmann M, Kampe B, Lehmann R, Totsche KU, Küsel K. Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Res. 2020;170:115341.CAS 
PubMed 

Google Scholar 
54.Mattes TE, Alexander AK, Richardson PM, Munk AC, Han CS, Stothard P, et al. The genome of Polaromonas sp. strain JS666: Insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Appl Environ Microbiol. 2008;74:6405–16.CAS 
PubMed 
PubMed Central 

Google Scholar 
55.Salinero KK, Keller K, Feil WS, Feil H, Trong S, Di Bartolo G, et al. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. BMC Genomics. 2009;10:1–23.
Google Scholar 
56.Kämpfer P, Schulze R, Jäckel U, Malik KA, Amann R, Spring S. Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol. 2005;55:341–4.PubMed 

Google Scholar 
57.Jin CZ, Zhuo Y, Wu XW, Ko SR, Li TH, Jin FJ, et al. Genomic and metabolic insights into denitrification, sulfur oxidation, and multidrug efflux pump mechanisms in the bacterium Rhodoferax sediminis sp. nov. Microorganisms. 2020;8:262.CAS 
PubMed Central 

Google Scholar 
58.Geisel N. Constitutive versus responsive gene expression strategies for growth in changing environments. PLoS ONE. 2011;6:e27033.CAS 
PubMed 
PubMed Central 

Google Scholar 
59.Boden R, Hutt LP, Rae AW. Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov within the ‘Proteobacteria’, and four new families within the orders Nitrosomonadales and Rhodocyclales. Int J Syst Evol Microbiol. 2017;67:1191–205.CAS 
PubMed 

Google Scholar 
60.Katayama-Fujimura Y, Tsuzaki N, Hirata A, Kuraishi H. Polyhedral inclusion-bodies (Carboxysomes) in Thiobacillus species with reference to the taxonomy of the genus Thiobacillus. J Gen Appl Microbiol. 1984;30:211–22.CAS 

Google Scholar 
61.Küsel K, Totsche KU, Trumbore SE, Lehmann R, Steinhäuser C, Herrmann M. How deep can surface signals be traced in the Critical Zone? Merging biodiversity with biogeochemistry research in a Central German Muschelkalk landscape. Front Earth Sci. 2016;4:32.
Google Scholar 
62.Roth VN, Lange M, Simon C, Hertkorn N, Bucher S, Goodall T, et al. Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nat Geosci. 2019;12:755–61.CAS 

Google Scholar 
63.Herrmann M, Wegner CE, Taubert M, Geesink P, Lehmann K, Yan LJ, et al. Predominance of Cand. Patescibacteria in groundwater is caused by their preferential mobilization from soils and flourishing under oligotrophic conditions. Front Microbiol. 2019;10:1407.PubMed 
PubMed Central 

Google Scholar 
64.Gray CM, Monson RK, Fierer N. Emissions of volatile organic compounds during the decomposition of plant litter. J Geophys Res Biogeosci. 2010;115:G03015.
Google Scholar 
65.Benk SA, Yan LJ, Lehmann R, Roth VN, Schwab VF, Totsche KU, et al. Fueling diversity in the subsurface: composition and age of dissolved organic matter in the Critical Zone. Front Earth Sci. 2019;7:296.
Google Scholar 
66.Schwab VF, Nowak ME, Elder CD, Trumbore SE, Xu XM, Gleixner G, et al. 14C-free carbon is a major contributor to cellular biomass in geochemically distinct groundwater of shallow sedimentary bedrock aquifers. Water Resour Res. 2019;55:2104–21.CAS 
PubMed 
PubMed Central 

Google Scholar 
67.Eiler A. Evidence for the ubiquity of mixotrophic bacteria in the upper ocean: Implications and consequences. Appl Environ Microbiol. 2006;72:7431–7.CAS 
PubMed 
PubMed Central 

Google Scholar 
68.Hansson TH, Grossart HP, del Giorgio PA, St-Gelais NF, Beisner BE. Environmental drivers of mixotrophs in boreal lakes. Limnol Oceanogr. 2019;64:1688–705.CAS 

Google Scholar 
69.Perez-Riverol Y, Csordas A, Bai JW, Bernal-Llinares M, Hewapathirana S, Kundu DJ, et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2019;47:D442–D50.CAS 
PubMed 

Google Scholar  More

Sub-regionsThe study region focuses on 18 sub-regions within the Pacific mountain ranges of North American overlapping with the range of Pacific Salmon with >1.5% glacier cover (Figs. 1 and 2). The term “sub-region” here refers to either a single major salmon watershed or aggregates of small coastal watersheds, which range in area from ~13,000 to ~68,000 km2. For sub-regions within Alaska, USA, we accessed boundary data from the Watershed Boundary Database at the USGS (https://www.usgs.gov/). For sub-regions within British Columbia, Canada, we accessed boundary data from the Freshwater Atlas of British Columbia (https://catalogue.data.gov.bc.ca/). Pacific salmon range data were from the National Center for Ecological Analysis and Synthesis (Fig. 1). The study region covers ~623,000 km2 across British Columbia, Canada and Alaska, USA and ~20% of the total North American range of Pacific salmon.Glacier outlinesOutlines for the 45,963 glaciers within the study region were obtained from the Randolph Glacier Inventory v6.0 (https://www.glims.org/RGI/; RGI v6.0), which provides a globally complete data set of glacier outlines outside of Greenland and Antarctic ice sheets17. These glaciers cover a total area of ~81,000 km2, which corresponds to 80% of the total glacier area in the Pacific mountain ranges within North America. The glacier outlines refer roughly to the years 2009 ± 2 for Alaska, and 2004 ± 5 for Western Canada17,53. Glacierization for each of 18 sub-regions ranges from 1.5 to 52%.Present-day streamsSynthetic stream networks were constructed from Digital Elevation Models (DEMs) for each of the 18 sub-regions using Geographic Information Systems (GIS; ArcGIS 10.6 and QGIS 2.18) hydrology tools to represent present-day streams throughout the study region. Specifically, we used Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) global DEMs v2.0 with a spatial resolution of ~30 m54. Open access synthetic stream network datasets such as the National Hydrography Dataset (NHD) from the USGS and the Freshwater Atlas from the British Columbia government are available but were not used due to inconsistencies in spatial resolution across the study region. From our synthetic stream networks, we eliminated all stream segments that overlapped with the RGI glacier outlines because the ASTER global DEMs used to create the synthetic stream networks represent glacier surface elevation rather than estimated deglaciated terrain. All present-day streams within our study region are void of any major dams that inhibit salmon movement based on existing databases of dams55. To summarize present-day stream kms, and all subsequent analyses, we used rstudio: 1.4.1103-4, R: ‘Mirrors’.Identifying and verifying stream gradient thresholds for migrating salmon and for determining accessible glaciersWe used stream gradient-based thresholds the determine constraints in salmon migration and the number of glaciers that would be accessible and create future streams for migrating adult salmon. Based on the large body of literature suggesting stream gradients (e.g., ranging from More