John Timothy Wootton

Research Summary
My research focuses on the ecological and evolutionary consequences of interactions among organisms. My work centers on how multi-species systems function and on evaluating methods that might predict how such systems will respond to environmental change, particularly in regard to the current epidemic of species extinctions and introductions occurring throughout the world and to global changes such as ocean acidification. I have conducted research on a wide variety of related subjects and retain active research interests in most of them, including the role of ecological factors on the evolution of life history and mating systems, and population viability models of endangered species. I work in several different systems, and study a range of taxa. My general approach develops and tests questions or models of broad theoretical interest, using field experiments, observations of large-scale species introductions, and between-system comparisons. Currently, my research focuses on rocky intertidal marine communities (particularly on Tatoosh Island, Washington) and rivers, which serve as model experimental systems for ecology. Visit for details
Experimental Community Ecology, Marine Ecology, Community Ecology, Quantitative Ecology, River Ecology, Conservation, Avian Ecology, Species Interaction, Food Web, Ecological Networks, Environmental Imact, Ocean Acidification, Ecosystems, Intertidal Ecology, Marine Invertebrates
  • Cornell University, Ithaca, New York, BS (Honors) Biology (Ecology, Systematics and Evolution) 05/1984
  • University of Washington, Seattle, Washington, Ph.D. Zoology 08/1990
  • University of California Berkeley, Berkeley, California, Integrative Biology 12/1992
Biosciences Graduate Program Association
Awards & Honors
  • 1990 - 1992 Miller Fellowship University of California, Berkeley
  • 1992 - Young Investigator Prize American Society of Naturalists
  • 1994 - Mercer Award Ecological Society of America
  1. Assessing predictions of population viability analysis: Peregrine Falcon populations in California. Ecol Appl. 2014; 24(6):1251-7. View in: PubMed

  2. Ecological Network Inference From Long-Term Presence-Absence Data. Sci Rep. 2017 08 02; 7(1):7154. View in: PubMed

  3. Intraspecific leaf chemistry drives locally accelerated ecosystem function in aquatic and terrestrial communities. Ecology. 2016 Aug; 97(8):2125-2135. View in: PubMed

  4. Functional Traits for Carbon Access in Macrophytes. PLoS One. 2016; 11(7):e0159062. View in: PubMed

  5. Historical baselines and the future of shell calcification for a foundation species in a changing ocean. Proc Biol Sci. 2016 06 15; 283(1832). View in: PubMed

  6. Diversity of Riparian Plants among and within Species Shapes River Communities. PLoS One. 2015; 10(11):e0142362. View in: PubMed

  7. Processes affecting extinction risk in the laboratory and in nature. Proc Natl Acad Sci U S A. 2015 Nov 03; 112(44):E5903. View in: PubMed

  8. What Can Interaction Webs Tell Us About Species Roles? PLoS Comput Biol. 2015 Jul; 11(7):e1004330. View in: PubMed

  9. Cascading effects of induced terrestrial plant defences on aquatic and terrestrial ecosystem function. Proc Biol Sci. 2015 Apr 22; 282(1805). View in: PubMed

  10. Local adaptation of stream communities to intraspecific variation in a terrestrial ecosystem subsidy. Ecology. 2014 Jan; 95(1):37-43. View in: PubMed

  11. Integrating the invisible fabric of nature into fisheries management. Proc Natl Acad Sci U S A. 2014 Jan 14; 111(2):581-4. View in: PubMed

  12. Experimental separation of genetic and demographic factors on extinction risk in wild populations. Ecology. 2013 Oct; 94(10):2117-23. View in: PubMed

  13. Complex population dynamics in mussels arising from density-linked stochasticity. PLoS One. 2013; 8(9):e75700. View in: PubMed

  14. Carbon system measurements and potential climatic drivers at a site of rapidly declining ocean pH. PLoS One. 2012; 7(12):e53396. View in: PubMed

  15. River food web response to large-scale riparian zone manipulations. PLoS One. 2012; 7(12):e51839. View in: PubMed

  16. Effects of timber harvest on river food webs: physical, chemical and biological responses. PLoS One. 2012; 7(9):e43561. View in: PubMed

  17. Rapid environmental change over the past decade revealed by isotopic analysis of the California mussel in the northeast Pacific. PLoS One. 2011; 6(10):e25766. View in: PubMed

  18. Predicting community responses to perturbations in the face of imperfect knowledge and network complexity. Ecology. 2011 Apr; 92(4):836-46. View in: PubMed

  19. The mixed mating system of the sea palm kelp Postelsia palmaeformis: few costs to selfing. Proc Biol Sci. 2011 May 07; 278(1710):1347-55. View in: PubMed

  20. Experimental species removal alters ecological dynamics in a natural ecosystem. Ecology. 2010 Jan; 91(1):42-8. View in: PubMed

  21. Treatment-based Markov chain models clarify mechanisms of invasion in an invaded grassland community. Proc Biol Sci. 2010 Feb 22; 277(1681):539-47. View in: PubMed

  22. Bobolink polygyny in a homogeneous habitat: a test of the asynchronous settlement model. Am Nat. 1992 Dec; 140(6):1050-7. View in: PubMed

  23. Dynamic patterns and ecological impacts of declining ocean pH in a high-resolution multi-year dataset. Proc Natl Acad Sci U S A. 2008 Dec 02; 105(48):18848-53. View in: PubMed

  24. Effects of disturbance on species diversity: a multitrophic perspective. Am Nat. 1998 Dec; 152(6):803-25. View in: PubMed

  25. Estimating nonlinear interaction strengths: an observation-based method for species-rich food webs. Ecology. 2008 Aug; 89(8):2083-9. View in: PubMed

  26. Understanding and predicting ecological dynamics: are major surprises inevitable? Ecology. 2008 Apr; 89(4):952-61. View in: PubMed

  27. Field parameterization and experimental test of the neutral theory of biodiversity. Nature. 2005 Jan 20; 433(7023):309-12. View in: PubMed

  28. An ecological approach to preventing human infection: vaccinating wild mouse reservoirs intervenes in the Lyme disease cycle. Proc Natl Acad Sci U S A. 2004 Dec 28; 101(52):18159-64. View in: PubMed

  29. Local interactions predict large-scale pattern in empirically derived cellular automata. Nature. 2001 Oct 25; 413(6858):841-4. View in: PubMed

  30. Productivity, consumers, and the structure of a river food chain. Proc Natl Acad Sci U S A. 1993 Feb 15; 90(4):1384-7. View in: PubMed

  31. Effects of productivity, consumers, competitors, and El Ni?o events on food chain patterns in a rocky intertidal community. Proc Natl Acad Sci U S A. 1996 Nov 26; 93(24):13855-8. View in: PubMed

  32. An experimental test of multi-species Markov models: Are barnacles long-term facilitators of mussel bed recovery?. Bulletin of Marine Science. 2013; 89:337-346.::::

  33. Using experimental indices to quantify the strength of species interactions. Oikos. 2010; 119:1057-1063.::::

  34. Marine Hard Bottom Communities: Patterns, Dynamics, Diversity and Change (Wahl M, ed.). Disruption, succession and stochasticity. 2009; 201-212.::::

  35. Small-scale genetic structure in the sea palm Postelsia palmaeformis Ruprecht (Phaeophyceae). Marine Biology. 2006; 139:731-742.::::

  36. Markov chain models predict the consequences of experimental extinctions. Ecology Letters. 2004; 7:653-660.::::

  37. The Importance of Species (Kareiva PM, Levin SA, eds.). Understanding the effects of reduced biodiversity: A comparison of two approaches. 2003; 85-104.::::

  38. Indirect effects in complex ecosystems: recent progress and future challenges. Journal of Sea Research. 2002; 48:157-172.::::

  39. Effects of disturbance on river food webs. Science. 1996; 273:1558-1561.::::

  40. Purple Finch. The Birds of North America. 1996; 208:1-20.::::

  41. Food Webs: Integration of Patterns and Dynamics (Polis GA, Winemiller KO, eds.). Disturbance and food chain length in rivers. 1996; 286-297.::::

  42. Effects of birds on sea urchins and algae: a lower-intertidal trophic cascade. Ecoscience. 1995; 2:321-328.::::

  43. Direct and indirect effects of Peregrine Falcon predation on seabird abundance. Auk. 1990; 107:1-9.::::

  44. The effects of body mass, phylogeny, habitat and trophic level on mammalian age at first reproduction. Evolution. 1987; 41:732-749.::::

  45. Interspecific competition between introduced House Finch populations and two associated passerine species. Oecologia. 1987; 71:325-331.::::

  46. Mating systems in homogeneous habitats: the effects of female uncertainty, knowledge costs, and random settlement. American Naturalist. 1986; 128:499-512.::::

  47. A metapopulation model of the Peregrine Falcon in California: viability and management strategies. Ecological Applications. 1992; 2:307-321.::::

  48. Indirect effects, prey susceptibility, and habitat selection: impacts of birds on limpets and algae. Ecology. 1992; 73:981-991.::::

  49. Ecological versus evolutionary hypotheses: demographic stasis and the Murray-Nolan clutch size equation. Evolution. 1991; 45:1947-1950.::::

  50. Bract liquid as an herbivore defense mechanism for Heliconia wagneriana inflorescences. Biotropica. 1990; 22:155-159.::::

  51. Clutch-size differences in western and introduced eastern populations of House Finches: patterns and hypotheses. Wilson Bulletin. 1986; 98:459-462.::::

  52. Encylopedia of Tidepools (Denny M, Gaines S, eds.). Birds. 2007; 91-95.::::

  53. Exploring B/Ca as a pH proxy for bivalves: relationships between Mytilus californianus B/Ca and environmental data from the northeast Pacific. Biogeosciences. 2011; 8:2567-2579.::::

  54. The relative roles of coastal and oceanic processes in determining physical and chemical characteristics of an intensively sampled nearshore system. Limnology and Oceanography. 2007; 52:1767-1775.::::

  55. Encylopedia of Tidepools (Denny M, Gaines S, eds.). Gulls. 2007; 252-255.::::

  56. Dominant (AFLP) and codominant (microsatellite) markers for the kelp Postelsia palmaeformis (Laminariales). Molecular Ecology Notes. 2004; 4:372-375.::::

  57. Theoretical concepts and empirical approaches to measuring interaction strength. Ecology. 1998; 79:461-476.::::

  58. Estimates and tests of per-capita interaction strength: diet, abundance, and impact of intertidally foraging birds. Ecological Monographs. 1997; 67:45-64.::::

  59. The nature and consequences of indirect effects in ecological communities. Annual Review of Ecology and Systematics. 1994; 25:443-466.::::

  60. Direct and indirect effects of nutrients on intertidal community structure: variable consequences of seabird guano. Journal of Experimental Marine Biology and Ecology. 1991; 151:139-153.::::

  61. The Ecology of Place (Billick I, Price M, eds.). A sense of place: Tatoosh. 2011; 229-250.::::

  62. Measurement of interaction strength in nature. Annual Review of Ecology, Evolution and Systematics. 2005; 36:419-444.::::

  63. Mechanisms of successional dynamics: consumers and the rise and fall of species dominance. Ecological Research. 2002; 17:249-260.::::

  64. Prediction in complex communities: analysis of empirically-derived Markov models. Ecology. 2001; 82:580-598.::::

  65. Hydraulic food chain models: an approach to the study of food web dynamics in large rivers. Bioscience. 1995; 45:159-167.::::

  66. Predicting direct and indirect effects: an integrated approach using experiments and path analysis. Ecology. 1994; 75:151-165.::::

  67. Food Webs: Structure, Stability and Ecosystem Functioning (de Ruiter P, Moore J, Wolters V, eds.). Trophic position, biotic context, and abiotic factors determine species contributions to ecosystem functioning. 2005; 295-307.::::

  68. Effects of substrate composition, stream-bed stability, and sediment supply on survival and trophic role of a dominant stream grazer. Verhandlungen der Internationalen Vereinigung für Theoretische und Angevandte Limnologie. 2002; 28:238:241.::::

  69. Issues and Perspectives in Experimental Ecology (Resetarits WJ, Bernardo J, eds.). The motivation of and context for experiments in ecology. 1998; 350-369.::::

  70. Causes of species diversity differences: a comparative analysis of Markov models. Ecology Letters. 2001; 4:46-56.::::

  71. Putting the pieces together: testing the independence of interactions among organisms. Ecology. 1994; 75:1544-1551.::::

  72. Size-dependent competition: effects on the dynamics versus the endpoint of mussel bed succession. Ecology. 1993; 74:195-206.::::

  73. Indirect effects and habitat use in an intertidal community: interaction chains and interaction modifications. American Naturalist. 1993; 141:71-89.::::

  74. Latitudinal differences in fish community trophic structure and the role of fish herbivory in a Costa Rican stream. Environmental Biology of Fishes. 1992; 35:311-319.::::

  75. Two male Bobolinks feed young at the same nest. Wilson Bulletin. 1986; 98:154-156.::::

  76. Longstanding signals of marine community structuring by winter storm wave-base. Marine Ecology Progress Series. 2018; 603:135-146.::::

  77. Characterizing species interactions: What is the community matrix?. Annual Review of Ecology, Evolution and Systematics. 2016; 47:409-432.::::

  78. A 20-year data set of species replacement patterns in the intertidal zone of Tatoosh Island, Washington, USA. Ecology. 2016; 97:810.::::

  79. Mutualism (Bronstein JL, ed.). Interaction strengths and mutualism. 143-144.::::

  80. Altered crystal mineralogy in the California mussel on decadal and centennial scales in a changing ocean. Global Change Biology. 2018; 24:2554-2562.::::

  81. Process catalyzers in Amazonian rivers: large woody debris modifies ecosystem processes across freshwater habitats. Ecosphere. 2018; 9:e2030.::::

  82. The iconic keystone predator has a pathogen. Frontiers in Ecology and the Environment. 2016; 14:285-286.::::

  83. The Ecology of Place (Billick I, Price M, eds.). A sense of place: Tatoosh. 229-250.::::

  84. Blanks in DIC analysis: long term storage effects on concentration and isotopic measurements using small sample sizes. Limnol. Oceanogr. Methods. 2018; 16:170-179.::::