ONLINE SUPPLEMENTAL MATERIAL: FIGURE S1
Figure S1. Temporal trends in the percentage of publications each year that contained the Web of Science topic ‘theor*’ for three leading ecology journals, beginning in the first publication year of the journal Ecosystems (1998). Lines represent least squares regressions for each journal; the slopes were 0.3% y-1 for The American Naturalist, 0.4% y-1 for Ecology, and -0.4% y-1 for Ecosystems.
ONLINE SUPPLEMENTAL MATERIAL: APPENDICES
APPENDIX 1. Examples demonstrating how theories comprise a series of postulates that logically lead to emergent conclusions more general than any one postulate. These postulates can then be tested with observations, experiments, and models.
A. Liebig’s Law of the Minimum, with thanks to Matt Ayres
Postulates
P1: Plant growth requires many different resources, including sunlight, water, carbon dioxide, nitrogen, phosphorus, and potassium.
P2: The relative availability of different essential resources may vary dramatically from site to site and year to year.
P3: Each resource fills unique physiological needs of the plant.
P4: One resource cannot be substituted for another.
Therefore, plant growth is limited by the one resource that is least available relative to the physiological needs of the plant. However, which resource is limiting can vary depending upon the environment.
B. Bioaccumulation and biomagnification, with thanks to Andrew Vacca
Postulates
P1: Food webs comprise distinct trophic levels with primary producers at the base and a series of sequential consumers that feed on lower trophic levels, moving energy and materials upwards.
P2: Energy moves into organisms through ingestion, is assimilated and allocated to growth, or lost in heat generation or respiration.
P3: Nutrients and other elements (including toxins) move into organisms through ingestion, are assimilated and stored in the body, or lost in waste excretion/egestion.
P4: Intake of contaminated materials and subsequent assimilation transports toxins into the body.
P5: Toxins accumulate in the body when assimilation occurs at a faster rate than removal.
P6: Higher rates of bioaccumulation occur with toxins that cannot be removed easily (or at all).
P7: Biomagnification occurs when organisms higher in the food web consume more contaminated food items.
Therefore, toxins bioaccumulate within organisms in association with the intake and assimilation of energy, but at rates determined by the ability of the body to remove the toxin via excretion or egestion. These toxins may then biomagnify along a trophic gradient, depending on the configuration of the food web’s producers and consumers and their ability to remove the toxin from the body.
APPENDIX 2. Theories applicable to ecosystem science. This list is intended to be illustrative, not exhaustive, and both the content and choice of citations reflect our bias toward ecosystem ecology. We encourage a grassroots effort to pull together a complete list available through an online repository, a distributed graduate seminar, or both.
Individual organisms, allometry and scaling
Marginal value theorem (Charnov 1976)
Metabolic theory of ecology (Brown and others 2004)
Dynamic energy budget theory (Kooijman 2009)
Eco-evolutionary dynamics (Post and Palkovacs 2009)
Trophic structure and species interactions
Trophic cascades (Paine 1980; Carpenter and others 1985)
Keystone species (Paine 1969, 1995; Power and others 1996)
Ecosystem engineering (Jones and others 1994, 1997)
Omnivory (Pimm and Lawton 1978; McCann and others 1998)
Green vs. brown webs (Wolkovich and others 2014; Zou and others 2016)
C-S-R theory (Grime 1977)
Stress gradient hypothesis (Bertness and Callaway 1994; Maestre and others 2009)
Trait-mediated indirect interactions (Abrams 1995; Werner and Peacor 2003)
Ecology of fear (Schmitz 2010)
Productivity and nutrient cycling
Laws of thermodynamics
Ecological stoichiometry (Sterner and Elser 2002)
Resource competition theory (Tilman 1982)
Bioaccumulation (Morel and others 1998)
Biodiversity-ecosystem function (Grime 1998; Loreau 2000; Loreau and others 2001)
Cross-system subsidies (Polis and others 1997 1997 )
Stability and disturbance
Succession (Clements1916; Connell and Slatyer, 1977)
Intermediate disturbance hypothesis (Connell 1978)
Resilience theory (Holling 1973; Scheffer and others 1993; Gunderson and Holling 2002)
Diversity-stability theory (McCann 2000; Cottingham and others 2001; Ives and Carpenter 2007)
Physical sciences
Greenhouse effect
Complexity theory (See www.santafe.edu/library/foundational-papers-complexity-science/)
Hierarchy theory (Allen and Starr 1982; O'Neill and others 1986)
Socio-ecological theory (See https://sesmad.dartmouth.edu/theories)
Tragedy of the commons (Hardin 1968)
Maximum sustainable yield (Russell 1931)
References for Appendix 2
Abrams PA. 1995. Implications of dynamically variable traits for identifying, classifying, and measuring direct and indirect effects in ecological communities. American Naturalist 146: 112-134.
Allen TFH, Starr TB. 1982. Hierarchy: Perspectives for Ecological Complexity. Chicago, Illinois, USA: University of Chicago Press.
Bertness MD, Callaway R. 1994. Positive interactions in communities. Trends In Ecology & Evolution 9: 191-193.
Brown JH, Gillooly JF, Allen AP, Savage VM, West GB. 2004. Toward a metabolic theory of ecology. Ecology 85: 1771-1789.
Carpenter SR, Kitchell JF, Hodgson JR. 1985. Cascading trophic interactions and lake productivity. Bioscience 35: 634-639.
Charnov EL. 1976. Optimal foraging, the marginal value theorem. Theoretical Population Biology 9: 129-136.
Clements FE. 1916. Plant succession: analysis of the development of vegetation. Carnegie Inst.Wash.Publ. 242: 1-512.
Connell JH. 1978. Diversity in tropical rain forests and coral reefs. Science 199: 1302-1310.
Connell JH, Slatyer RO. 1977. Mechanisms of succession in natural communities and their role in community stability and organization. American Naturalist 111: 1119-1144.
Cottingham KL, Brown BL, Lennon JT. 2001. Biodiversity may regulate the temporal variability of ecological systems. Ecology Letters 4: 72-85.
Grime JP. 1977. Evidence for existence of three primary strategies in plants and its relevance to ecological and evolutionary theory. American Naturalist 111: 1169-1194.
Grime JP. 1998. Benefits of plant diversity to ecosystems: immediate, filter and founder effects. Journal of Ecology 86: 902-910.
Gunderson LH, Holling CS editors. 2002. Panarchy: Understanding Transformation in Human and Natural Systems. Washington, D.C.: Island Press.
Hardin G. 1968. The tragedy of the commons. Science 162: 1243-1248.
Holling CS. 1973. Resilience and stability of ecological systems. Annual Review of Ecology and Systematics 4: 1-23.
Ives AR, Carpenter SR. 2007. Stability and diversity of ecosystems. Science 317: 58-62.
Jones CG, Lawton JH, Shachak M. 1994. Organisms as ecosystem engineers. Oikos 69: 373-386.
Jones CG, Lawton JH, Shachak M. 1997. Positive and negative effects of organisms as physical ecosystem engineers. Ecology 78: 1946-1957.
Kooijman SALM. 2009. Dynamic Energy Budget Theory for Metabolic Organisation. New York, NY: Cambridge University Press.
Loreau M. 2000. Biodiversity and ecosystem functioning: recent theoretical advances. Oikos 91: 3-17.
Loreau M, Naeem S, Inchausti P, Bengtsson J, Grime JP, Hector A, Hooper DU, Huston MA, Raffaelli D, Schmid B, Tilman D, Wardle DA. 2001. Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294: 804-808.
Maestre FT, Callaway RM, Valladares F, Lortie CJ. 2009. Refining the stress-gradient hypothesis for competition and facilitation in plant communities. Journal of Ecology 97: 199-205.
McCann K, Hastings A, Huxel GR. 1998. Weak trophic interactions and the balance of nature. Nature 395: 794-798.
McCann KS. 2000. The diversity-stability debate. Nature 405: 228-233.
Morel FMM, Kraepiel AML, Amyot M. 1998. The chemical cycle and bioaccumulation of mercury. Annual Review of Ecology and Systematics 29: 543-566.
O'Neill RV, DeAngelis DL, Waide JB, Allen TFH. 1986. A Hierarchical Concept of Ecosystems. Princeton, New Jersey, USA: Princeton University Press.
Paine RT. 1969. A note on trophic complexity and community stability. American Naturalist 103: 91-93.
Paine RT. 1980. Food webs: linkage, interaction strength and community infrastructure. Journal of Animal Ecology 49: 667-685.
Paine RT. 1995. A conversation on refining the concept of keystone species. Conservation Biology 9: 962-964.
Pimm SL, Lawton JH. 1978. On feeding on more than one trophic level. Nature 275: 542-544.
Polis GA, Anderson WB, Holt RD. 1997. Toward an integration of landscape and food web ecology: The dynamics of spatially subsidized food webs. Annual Review of Ecology and Systematics 28: 289-316.
Post DM, Palkovacs EP. 2009. Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play. Philosophical Transactions of the Royal Society B-Biological Sciences 364: 1629-1640.
Power ME, Tilman D, Estes JA, Menge BA, Bond WJ, Mills LS, Daily G, Castilla JC, Lubchenco J, Paine RT. 1996. Challenges in the quest for keystones. Bioscience 46: 609-620.
Russell ES. 1931. Some theoretical considerations on the ‘overfishing’ problem. Journal de Conseil International pour l’Explaration de la mer 6: 1-20.
Scheffer M, Hosper SH, Meijer ML, Moss B, Jeppesen E. 1993. Alternative equilibria in shallow lakes. Trends in Ecology and Evolution 8: 275-279.
Schmitz OJ. 2010. Resolving Ecosystem Complexity. Princeton, NJ: Princeton University Press.
Sterner RW, Elser JJ. 2002. Ecological Stochiometry: The Biology of Elements from Molecules to the Biosphere. Princeton, NJ Princeton University Press.
Tilman D. 1982. Resource Competition and Community Structure. Princeton, NJ: Princeton.
Werner EE, Peacor SD. 2003. A review of trait-mediated indirect interactions in ecological communities. Ecology 84: 1083-1100.
Wolkovich EM, Allesina S, Cottingham KL, Moore JC, Sandin SA, de Mazancourt C. 2014. Linking the green and brown worlds: the prevalence and effect of multichannel feeding in food webs. Ecology 95: 3376-3386.
Zou K, Thébault E, Lacroix G, Barot S. 2016. Interactions between the green and brown food web determine ecosystem functioning. Functional Ecology: in press.
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