About

John Timothy Wootton is a Professor of Ecology and Evolution at the University of Chicago. His research focuses on the ecological and evolutionary consequences of interactions among organisms, with particular attention to how multi-species systems function and how they respond to environmental change. His work addresses issues such as species extinctions, introductions, and global changes like ocean acidification. Wootton's research spans various systems and taxa, employing field experiments, observations, and comparative analyses to develop and test broad theoretical models. Currently, he concentrates on rocky intertidal marine communities, especially around Tatoosh Island, Washington, and river ecosystems, which serve as model systems for ecological studies.

Research topics

• Ecology
• Biology
• Environmental science
• Geography
• Computer science

Selected publications

• Spatially Varying Selection Amplifies Intrapopulation Differentiation Among Phenotypic Traits in the Rocky‐Shore Mussel, <i>Mytilus californianus</i>

  Ecology and Evolution · 2025-06-30 · 1 citations

  articleOpen access

  ABSTRACT Strong ecological gradients along heterogeneous environments play an important role in shaping population differentiation across species ranges. Thus, the selective pressure of environmental variation on phenotypic variation strongly affects an organism's ability to persist across diverse or new environments. We investigated the spatial variability of biological responses in the intertidal bivalve Mytilus californianus to highlight the costs and trade‐offs of local adaptation and phenotypic plasticity across various functional traits in a dynamic environment, the marine intertidal. To test this, we performed a reciprocal transplant experiment with M. californianus individuals originating from the upper and lower intertidal measuring relevant phenotypic traits, followed by whole genome sequencing (WGS). We determined that morphological traits in individuals demonstrated phenotypic plasticity when moved to new environments, whereas physiological traits such as metabolism exhibited constraints in plasticity. Additionally, mussels from high intertidal zones, which experience greater heat and aerial exposure stress, maintained lower metabolic rates and showed increased frequencies of non‐synonymous mutations in functionally relevant heat shock proteins when compared to low intertidal mussels. These results suggest that morphological and physiological traits responded differently to spatially varying selection within the marine intertidal.

  PublisherOA PDFDOI

• Slower environmental cycles maintain greater life‐history variation within populations

  Ecology Letters · 2021-09-02 · 13 citations

  letterOpen accessSenior author

  Populations in nature are comprised of individual life histories, whose variation underpins ecological and evolutionary processes. Yet the forces of environmental selection that shape intrapopulation life-history variation are still not well-understood, and efforts have largely focused on random (stochastic) fluctuations of the environment. However, a ubiquitous mode of environmental fluctuation in nature is cyclical, whose periodicities can change independently of stochasticity. Here, we test theoretically based hypotheses for whether shortened ('Fast') or lengthened ('Slow') environmental cycles should generate higher intrapopulation variation of life history phenotypes. We show, through a combination of agent-based modelling and a multi-generational laboratory selection experiment using the tidepool copepod Tigriopus californicus, that slower environmental cycles maintain higher levels of intrapopulation variation. Surprisingly, the effect of environmental periodicity on variation was much stronger than that of stochasticity. Thus, our results show that periodicity is an important facet of fluctuating environments for life-history variation.

  PublisherOA PDFDOI

• Purple Finch (Haemorhous purpureus)

  Birds of the World · 2020-03-04 · 2 citations

  reference-entry1st authorCorresponding
  PublisherDOI

• Reconciling empirical interactions and species coexistence

  Ecology Letters · 2019-03-22 · 16 citations

  article

  Coexistence in ecological communities is governed largely by the nature and intensity of species interactions. Countless studies have proposed methods to infer these interactions from empirical data, yet models parameterised using such data often fail to recover observed coexistence patterns. Here, we propose a method to reconcile empirical parameterisations of community dynamics with species-abundance data, ensuring that the predicted equilibrium is consistent with the observed abundance distribution. To illustrate the approach, we explore two case studies: an experimental freshwater algal community and a long-term time series of displacement in an intertidal community. We demonstrate how our method helps recover observed coexistence patterns, capture the core dynamics of the system, and, in the latter case, predict the impacts of experimental extinctions. Collectively, these results demonstrate an intuitive approach for reconciling observed and empirical data, improving our ability to explore the links between species interactions and coexistence in natural systems.

  PublisherDOI

• The Origin, Succession, and Predicted Metabolism of Bacterial Communities Associated with Leaf Decomposition

  mBio · 2019-09-04 · 26 citations

  articleOpen accessSenior author

  Community ecologists have traditionally treated individuals within a species as uniform, with individual-level biodiversity rarely considered as a regulator of community and ecosystem function. In our study system, we have documented clear evidence of within-species variation causing local ecosystem adaptation to fluxes across ecosystem boundaries. In this striking pattern of a "home-field advantage," leaves from individual trees tend to decompose most rapidly when immediately adjacent to their parent tree. Here, we merge community ecology experiments with microbiome approaches to describe how bacterial communities adjust to within-species variation in leaves over spatial scales of less than a kilometer. The results show that bacterial community compositional changes facilitate rapid ecosystem responses to environmental change, effectively maintaining high rates of carbon and nutrient cycling through ecosystems.

  PublisherDOI

• Process catalyzers in Amazonian rivers: large woody debris modifies ecosystem processes across freshwater habitats

  Ecosphere · 2018-01-01 · 6 citations

  articleOpen accessSenior author

  Abstract Understanding the role of interactions in influencing community structure and ecosystem function is a goal in ecology, and identifying biotic entities that are strong interactors is imperative for setting targeted conservation strategies. Several different mechanisms have been linked with strongly interacting species (e.g., predation, competition, abiotic habitat modification), but the most important organisms often influence ecosystems in multiple ways. We propose that these strong interactors share a broad common feature: They catalyze ecosystem processes, such as rates of primary productivity, species interactions, and/or physical disturbances. We provide a case study of Spanish cedar ( Cedrela odorata ), focusing on its influence as a provider of large woody debris ( LWD ) on food web dynamics in tropical floodplain rivers and associated oxbow lakes. Large woody debris has been subject to considerable attention because of its perceived importance in creating geomorphologically favorable conditions for target commercial species (e.g., distribution of pools and riffle for salmonids). However, in this study we suggest that LWD catalyzes a suite of ecological processes in addition to geomorphology that determines its important role within aquatic communities. Through a factorial experiment manipulating large and small fish access to treatments with and without LWD piles, we tested the role of Spanish cedar in modifying interactions between different‐sized fishes, invertebrates, and primary producers in a tropical floodplain river and associated oxbow lake. Path analysis revealed that fishes influence particulate matter accumulation and invertebrate abundances more so in wood piles than outside of wood piles in both river and lake ecosystem contexts. In addition to providing the first experimental test of factors controlling trophic dynamics in an Amazonian river, we suggest that understanding the role of organisms through the ecological processes they catalyze provides an overarching conceptual framework to link single species and ecosystem‐based management strategies.

  PublisherDOI

• A mineralogical record of ocean change: Decadal and centennial patterns in the California mussel

  Global Change Biology · 2018-01-04 · 24 citations

  articleOpen access

  Ocean acidification, a product of increasing atmospheric carbon dioxide, may already have affected calcified organisms in the coastal zone, such as bivalves and other shellfish. Understanding species' responses to climate change requires the context of long-term dynamics. This can be particularly difficult given the longevity of many important species in contrast with the relatively rapid onset of environmental changes. Here, we present a unique archival dataset of mussel shells from a locale with recent environmental monitoring and historical climate reconstructions. We compare shell structure and composition in modern mussels, mussels from the 1970s, and mussel shells dating back to 1000-2420 years BP. Shell mineralogy has changed dramatically over the past 15 years, despite evidence for consistent mineral structure in the California mussel, Mytilus californianus, over the prior 2500 years. We present evidence for increased disorder in the calcium carbonate shells of mussels and greater variability between individuals. These changes in the last decade contrast markedly from a background of consistent shell mineralogy for centuries. Our results use an archival record of natural specimens to provide centennial-scale context for altered minerology and variability in shell features as a response to acidification stress and illustrate the utility of long-term studies and archival records in global change ecology. Increased variability between individuals is an emerging pattern in climate change responses, which may equally expose the vulnerability of organisms and the potential of populations for resilience.

  PublisherOA PDFDOI

• Seawater DIC analysis: The effects of blanks and long‐term storage on measurements of concentration and stable isotope composition

  Limnology and Oceanography Methods · 2018-01-17 · 14 citations

  articleOpen accessSenior author

  Abstract Dissolved inorganic carbon (DIC) concentration and stable isotope composition measurements (δ 13 C) are central to the study of biological and chemical processes in the ocean. We examined a small volume (1 mL) method using continuous‐flow isotope ratio mass spectrometry (CF‐IRMS) for making both measurements in a single sample run. Prior exploration of this approach has yielded variable results. Effects of concentration, isotopic composition, storage time, and the gas used to flush the sample tubes were tested using standard solutions. Multiple isotopic composition standards permitted calculation of an apparent blank that develops due to slow rates of gas exchange through the septum. A blank correction is applied to the δ 13 C measurements, giving precision and accuracy better than 0.1‰ after 6 months of storage and ∼ 0.2‰ after 18 months of storage. CF‐IRMS concentration measurements on field samples collected near Tatoosh Island, off the Pacific coast of Washington, U.S.A., were compared to independent measurements (Dickson, CDQC Laboratory, UCSD) on the same water, the latter approach involving collection of 500 mL of seawater fixed with mercuric chloride. Concentration measurements by CF‐IRMS on seawater samples (precision ∼ 1–2%) are correctable to the Dickson results, though scatter in this relation exceeds analytical precision. The DIC and δ 13 C measurements on coastal seawater, in conjunction with salinity measurements, indicated strong effects of biological activity on carbon dynamics relative to possible effects of mixing water masses. In sum, this small volume methodology has application to field situations and laboratory experiments where larger volumes are logistically challenging and storage space is limited.

  PublisherOA PDFDOI

• Ecological Network Inference From Long-Term Presence-Absence Data

  Scientific Reports · 2017-07-27 · 67 citations

  articleOpen access

  Ecological communities are characterized by complex networks of trophic and nontrophic interactions, which shape the dy-namics of the community. Machine learning and correlational methods are increasingly popular for inferring networks from co-occurrence and time series data, particularly in microbial systems. In this study, we test the suitability of these methods for inferring ecological interactions by constructing networks using Dynamic Bayesian Networks, Lasso regression, and Pear-son's correlation coefficient, then comparing the model networks to empirical trophic and nontrophic webs in two ecological systems. We find that although each model significantly replicates the structure of at least one empirical network, no model significantly predicts network structure in both systems, and no model is clearly superior to the others. We also find that networks inferred for the Tatoosh intertidal match the nontrophic network much more closely than the trophic one, possibly due to the challenges of identifying trophic interactions from presence-absence data. Our findings suggest that although these methods hold some promise for ecological network inference, presence-absence data does not provide enough signal for models to consistently identify interactions, and networks inferred from these data should be interpreted with caution.

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• Appendix A. Questionnaire that was e-mailed to 113 experienced field ecologists.

  Figshare · 2016-01-01

  datasetOpen access

  Questionnaire that was e-mailed to 113 experienced field ecologists.

  PublisherDOI

Recent grants

• LTREB Renewal: Ecological Dynamics in an Experimentally-Tractable Natural Ecosystem

  NSF · $448k · 2016–2022

• LTREB: Ecological Dynamics in an Experimentally-Tractable Natural Ecosystems

  NSF · $440k · 2009–2015

• Effects of Demography and Genetics on Extinction in Small Populations: Experiments with an Exploited Kelp

  NSF · $756k · 2001–2006

• Dissertation Research: Quantitative Interaction Strengths in Omnivorous Food Webs Across a Gradient in Primary Productivity

  NSF · $12k · 2006–2008

• DISSERTATION RESEARCH: Drivers and Consequences of Intraspecific Trait Variation: Ecology of a Forest-Stream Community

  NSF · $21k · 2013–2015

Frequent coauthors

• Catherine A. Pfister

  University of Chicago

  30 shared

• María G. Luna

  20 shared

• Durland Fish

  Yale University

  16 shared

• Jean I. Tsao

  Michigan Department of Natural Resources

  16 shared

• Alan G. Barbour

  University of California, Irvine

  16 shared

• Jonas Bunikis

  University of California, Irvine

  16 shared

• Mary E. Power

  University of California, Berkeley

  15 shared

• Márk Novák

  Oregon State University

  13 shared

Labs

• Wootton Lab at the University of ChicagoPI

Education

• Ph.D., Zoology

  University of Washington

  1990

• Other, Biology (Ecology, Systematics and Evolution)

  Cornell University

  1984

• Other

  University of California Berkeley

  1992

Awards & honors

• Mercer Award Ecological Society of America (1994)
• Young Investigator Prize American Society of Naturalists (19…
• Miller Fellowship University of California, Berkeley (1990 -…