Previous Graduate Students

JONATHAN CHASE:  Jon was co-advised by Mathew Leibold.  His Ph. D. project focused on how size-dependent interactions affect food web structure and response to ecosystem productivity.  He documented a curious pattern of snail abundance and plant biomass across a phosphorous-controlled productivity gradient, characterized by low plants, weak grazer control, and dominance by Physa at low productivity, high plants, strong grazer control, and dominance by Helisoma at high productivity, but a mixture of these different states in different ponds with intermediate productivity.  He also demonstrated that Physa and small Helisoma were readily consumed by predators but that large Helisoma were not.  From these results, he postulated that size-dependent predation was leading to alternative stable states at intermediate productivity, with ponds in some cases being under strong predator control and others dominated by predator-resistant grazers.  Food web models with size-structured predation demonstrated, contrary to prior verbal theory, that size structure alone could not produce alternative stable states (although the system can stay close to an unstable equilibrium for long periods in transient dynamics), but that a configuration including an edible competitor species could generate  alternative stable states at intermediate productivity.  He then carried out studies in replicated experimental ponds by varying productivity, predator presence, and the initial densities of snails, which demonstrated the predicted shift in food web structure and alternative stable states at intermediate levels.  This work is one of the best examples of alternative stable states yet in ecology.  Jon also carried out many side-projects, including studies of small-scale variation in grassland food chains, and behavior-mediated effects of tadpoles in rivers.  He also began exploring the interplay of disturbance, productivity, and food web structure, the niche concept and effects of local and regional processes on community composition.  Jon subsequently joined the faculty of Washington University, Saint Louis. and is currently is at Martin Luther University in Germany, where he is part of the German Centre for Integrative Biodiversity Research. Publications that involved work done while a student at U of Chicago include:

Chase, J. M. 2003. Experimental evidence for alternative stable equilibria in a benthic pond food web. Ecology Letters 6:733-741.

Chase, J. M. 2003. Strong and weak trophic cascades along a productivity gradient. Oikos. 101: 187-195.

Chase, J. M. and M. A. Leibold.  2002. Spatial scale dictates the productivity-biodiversity relationship. Nature 416:427-430.

Chase J.M., M. A. Leibold, A. L. Downing, and J. B. Shurin. 2000. The effects of productivity, herbivory, and plant species turnover in grassland food webs. Ecology 81:2485-2497.

Leibold, M.A.., J.M. Chase, J. B. Shurin, and A. L. Downing. 1997. Species turnover and the regulation of trophic structure. Annual Review of Ecology and Systematics 28:467-494.

Chase, J. M., M. A Leibold, and E. Simms.  2001. Plant tolerance and resistance in food webs: Community-level predictions and evolutionary implications. Evolutionary Ecology 14:289-314.

Chase, J. M., and M. A. Leibold.  2001.  Ecological Niches:  Linking Classical and Contemporary Approaches.  University of Chicago Press. 

Chase, J. M., W. G. Wilson, and S. A. Richards, Shane.  2001.  Foraging trade-offs and resource patchiness: Theory and experiments with a freshwater snail community. Ecology Letters 4: 304-312.

Chase, J. M. 1999. To grow or to reproduce? The role of life-history plasticity in food web dynamics. American Naturalist 154:571-586.

Chase, J. M. 1999. Food web effects of prey size refugia: Variable interactions and alternative stable equilibria.  American Naturalist 154: 559-570.

Chase, J. M. 1998. Central-place forager effects on food web dynamics and spatial pattern in northern California meadows.  Ecology 79:1236-1245.


JEAN TSAO:  Jean has a strong interest in the interface of ecological science and human health, and developed an ambitious project to examine this issue in a particularly appropriate system:  Lyme Disease.  She set out to experimentally test the hypothesis of Rick Ostfeld and colleagues that the ecological community comprising the backdrop for the disease could have strong effects on disease prevalence.  To do this, she worked closely with the laboratories of Durland Fish (Yale University) and Alan Barbour (University of California, Irvine) to generate an experimental host “species”:  white-footed mice vaccinated against Lyme Disease.  This experiment was implemented on large-scale plots (100 x 100 m) and the subsequent dynamics of the disease, tick populations, and mouse populations were monitored.  She then incorporated the results into a mechanistic model of host-disease ecology and systematically considered whether key features of the model (mouse density, vaccination treatment, contributions of mice to tick production) were necessary to produce her experimental results.  She found that disease levels were depressed as predicted by the host community hypothesis following mouse vaccination, and that the response was strongly tied to mouse density.  These results suggest that if it can be effectively deployed (e.g, via digestion with food), field vaccination of hosts or other methods of manipulating the host community may be helpful in fighting the disease.  Additionally, her results revealed that Lyme Disease levels are strongly influenced by alternative hosts to mice, in contrast to conventional wisdom.  These responses were complex, such that if alternative hosts were lost via local or regional extinction, disease levels are likely to increase.  Jean is now on the faculty of Michigan State University.  Publications involving work done while at U of Chicago include:

Tsao, J. I., J. T. Wootton, J. Bunikis, M. G. Luna, D. Fish, and A. G. Barbour.  2004.  An ecological approach to preventing human infection:  vaccinating wild mouse reservoirs intervenes in the Lyme disease cycle. Proceedings of the National Academy of Science 52:18159-18164

Bunikis, J., J. Tsao, C. J. Luke, M. G. Luna, D. Fish, and A. G. Barbour.  2004. Borrelia burgdorferi infection in a natural population of Peromyscus leucopus mice: A longitudinal study in an area where lyme borreliosis is highly endemic. Journal of Infectious Diseases 189:1515-1523.

Tsao, J., A. Barbour, C. Luke, E. Fikrig, D. Fish. 2001. Inoculation with OspA causes a decrease in transmission of Borrelia burgdorferi from infected Peromyscus leucopus to larval Ixodes scapularis. Vect. Born. Zoon. Dis., 1:65-74.

AMY DOWNING:  Amy was co-advised by Mathew Leibold.  Her Ph. D. investigated the link between biodiversity and ecosystem function and stability, using experimental pond communities.  Prior work on this problem involved either single trophic level systems (plants) or was restricted to laboratory settings.  Amy’s projected extended investigations into the realm of multi-trophic situations characteristic of real ecosystems.  She varied the diversity of predators, grazers, and macrophytes in a variety of combinations to explore how overall diversity affected system productivity, respiration, chemical characteristics, and the resistance and resilience of the system in response to pulsed perturbations (changes in pH or nutrients, mimicking pulsed runoff events observed in many areas).  She found general patterns of increase in ecosystem function with diversity.  Because she replicated the species composition of her diversity treatments, Amy’s study was also unique in its ability to tease apart the effects of species identity versus overall diversity.  Her results indicate that most of the diversity effect is the result of species-specific contributions and strong synergisms among key combinations of species, and she was able to identify some of the species causing disproportionately large effects on the system.  Surprisingly, consumer species generally had the strongest effects on ecosystem processes, although they are more distantly removed from many of them compared to the plant species she manipulated.  Amy is now on the faculty of Ohio Wesleyan University.  Publications involving work done while at U. of Chicago include:

Downing, A. L., and M. A. Leibold. 2010. Species richness facilitates ecosystem resilience in aquatic food webs. Freshwater Biology 10:2123-2137.

Downing, A. L., and J. T. Wootton. 2005. Trophic position, biotic context, and abiotic factors determine species contributions to ecosystem functioning. Pp. 295-307 in P. de Ruiter, J. Moore, and V. Wolters, editors. Dynamic Food Webs: Multispecies assemblages, ecosystem development, and environmental change. Academic Press.

Downing, A. L. 2005. Relative effects of species composition and richness on pond ecosystem properties in ponds. Ecology 86: 701-715.

Petchey, O. L., A. L. Downing, G. G. Mittelbach, L. Persson, C. F. Steiner, P. H. Warren, and G. Woodward.  2004. Species loss and the structure and functioning of multitrophic aquatic systems. Oikos 104: 467-478

Downing, A. L. and M. A. Leibold.  2002. Ecosystem consequences of species richness and composition in pond food webs.  Nature 416:837-841.

Loreau, M., A. Downing, M. Emmerson, A. Gonzalez, J. Hughes, P. Inchausti, J. Joshi, J. Norberg and O. Sala. 2002. In A new look at the relationship between diversity and stability. In M. Loreau, S. Naeem, and P. Inchausti, eds. Biodiversity and Ecosystem Functioning: Synthesis and Perspectives. Oxford University Press.

Wootton, J. T. and A. Downing. 2002. Understanding the Effects of Reduced Biodiversity: A Comparison of Two Approaches, In P. Kareiva, and S. Levin eds.  The Importance of Species: Perspectives on Expendability and Triage. Princeton University Press.

Chase J.M., M. A. Leibold, A. L. Downing, and J. B. Shurin. 2000. The effects of productivity, herbivory, and plant species turnover in grassland food webs. Ecology 81:2485-2497.

Leibold, M.A., J.M. Chase, J. B. Shurin, and A. L. Downing. 1997. Species turnover and the regulation of trophic structure. Annual Review of Ecology and Systematics. 28: 467-494.

KEVIN BRITTON-SIMMONS:  Kevin’s research focused on the invasion dynamics and community impacts of an invasive brown seaweed, Sargassum muticum, in subtidal marine communities.  Sargassum is steadily invading the Puget Sound area of Washington State and other areas, following its introduction from Japan.  Sargassum has a dual mode of dispersal with very local production of gametophytes and long-distance rafting of attached adults.  To investigate invasion dynamics, Kevin studied invasion fronts of Sargassum and carried out manipulations that demonstrated that invasion speed was negatively affected by dispersal limitation of Sargassum embryos and by interactions with native species when they were present in key combinations of functional groups (encrusting species to preempt recruitment to empty space, canopy species to cast shade on established recruits).  Once established, Sargassum strongly reduced native kelp species, which indirectly resulted in reduced sea urchin abundance as their food source was decreased.  Finally, he showed that habitat heterogeneity facilitated coexistence of natives and the invader, with Sargassum performing very poorly on vertical surfaces, which allowed natives to persist.  Kevin was affiliated with the Friday Harbor Laboratories at the University of Washington, and now is Chairman of the Board of his family’s business.  Publications involving work done while at U. of Chicago include:

Britton-Simmons, K. H., and K. C. Abbott. 2008. Short- and long-term effects of disturbance and propagule pressure on a biological invasion. J. Ecology.  96:68-77.

Britton-Simmons, K. H.  2006.  Functional group diversity, resource preemption and the genesis of invasion resistance in a marine algae.   Oikos 113:395-401.

Klinger, T., D. K. Padilla and K. Britton-Simmons. 2006. Two invaders achieve higher densities in marine reserves. Aquatic Conservation.  16:301-313.

Britton-Simmons, K. H.  2004.  Direct and indirect effects of the introduced alga Sargassum muticum on benthic, subtidal communities of Washington State, USA.  Mar. Ecol. Prog. Ser. 277: 61-78.


PAMELA GEDDES:  Pam was co-advised by Mathew Leibold.  She became interested in the role that external subsidies into systems play in shaping community structure and stability, and focused on ponds across a range of forest cover.  Her thesis project emphasized the dissolved organic matter contributed by leaves to ponds, particularly released humic substances that can stain water brown (e.g., tea generated from tea leaves).  Experiments in experimental pond mesocosms showed that community structure shifted with the addition of humic substances and that, contrary to theory, system stability decreased.  Subsequent experiments manipulating the variability of input into the system unexpectedly failed to increase the system variability, suggesting strong homeostatic mechanisms within the food web.  Finally, small-scale experiments designed to tease apart mechanisms of action by humic substances by varying zooplankton contact with enriched water and incident UV light indicated that they had strong short-term effects on the food web via non trophic pathways, including providing protection from UV radiation and introducing detrimental defensive compounds into the water.  Pam is currently on the faculty of Northeastern Illinois University.

Leibold, M. A., and P. Geddes   2005.  The niche concept in metacommunities.  Ecologia Austral 15:117-129.

Geddes, P.  2009.  Decoupling carbon effects and UV protection from terrestrial subsidies on pond zooplankton.   Hydrobiologia 628:47-66.

DOUG NUTTER Doug was co-advised with Cathy Pfister.  Doug explored several factors affecting the structure of tidepool communities.  One aspect of his study was to test the hypothesis of community-assembly for multi-trophic systems put forward by Bob Holt, which predicts steeper species accumulation curves with area by consumers compared to plant species because prey need to invade an area before populations of their consumers can be sustained.  Using experimental tidepools of different size, Doug found only a weak trend following this pattern, suggesting that several fundamental assumptions of the theory (closed systems, lack of feedback by consumers on prey diversity, lack of strong competitive interactions among species at a single trophic level) may be violated in real systems.  He also experimentally investigated the nature of disturbances and stress to systems, focusing on the relative importance of intensity and frequency of events.  By varying the delivery rate and mean concentration of ammonium, a toxic compound when found at high concentrations when delivered from coastal sources such as runoff from seabird and marine mammal waste, he found that the intensity of disturbance plays a much stronger role than the temporal variation of disturbance.  Doug is now in the Department of Natural Resources and Director of Institutional Research at Bowie State University.

LISA (LIS) CASTILLO NELIS: Lis studied  how the invasion of exotic species affects the community structure through reorganization of the web of interactions among species.  Her thesis project explored how synergistic interactions among invaders affect invasion dynamics, focusing on the invasion of exotic plants, and European Rabbits on the remote islands of the Juan Fernandez Archipelago (“Robinson Crusoe Islands”) off the coast of Chile.  Plant invasion was affected by soil disturbance and the introduction of rabbits, which may change competition with natives via grazing and digging, disperse seeds of some invaders on their fur, and alter nutrient cycling on the landscape through burrowing and fecal deposition.  Lis conducted large (10 x 10 m) experimental manipulations of rabbits, trun, and native species to tease apart these invasion dynamics, combining experimental results with mathematical modeling to explore the success of native and invasive plants.  Her experiments and analyses using Markov chain models suggest that simply removing rabbits will not benefit native species, and that invasive plant species are characterized by idiosyncratic traits related to co-evolutionary history with grazers and to general population dynamics, rather than general patterns common to all invaders. Lis went on to a post-doctoral fellow at Stanford and is now a Senior Scientist at Exponent.

Nelis, L. C. 2012.  Life form and life history explain variation in population processes of a grassland community invaded by exotic plants and animals.  PLoS ONE 7(8): e42906. doi:10.1371/journal.pone.0042906

Nelis, L. C.  2012.
Grouping plant species by shared native range, and not by native status, predicts response to an exotic herbivore.  Oecologia 169:1075-1081. doi:10.1007/s00442-012-2265-4

Nelis, L. C., and J. T. Wootton. 2010.  Treatment-based Markov chain models clarity mechanisms of invasion in an invaded grassland community. Proceedings of the Royal Society Biological Sciences Series B 277:539-547.

MARK NOVAK:  Mark focused on the role of omnivory on food web dynamics and the patterns of interaction strength throughout communities.  He studied these questions experimentally and with stable isotope methods in the intertidal zone of New Zealand, which is relatively unstudied and has a somewhat different structure than well-studied North American systems.  He took advantage of the strong gradient in productivity generated by shifts in coastal upwelling to determine whether omnivory shifts with productivity as expected by theory, and how this shift affects community stability.  In the process, he also developed and experimentally tested an approach to use feeding observations to estimate interaction strengths of consumers in multi-species systems. He found that changes in abundance along the productivity gradient were inconsistent with current predictions of intragulid predation theory, apparently because of interference interactions among basal resources and adaptive changes in diet composition with productivity. He also found that, although predator feeding followed non-linear multispecies functional responses in the laboratory, the range of prey abundance encountered in nature was sufficiently narrow that consumption rates follow a roughly linear relationship with prey, as in classical ecological models. Mark is now on the faculty of Oregon State University. Publications involving work done while at U. Chicago include:

M. Novak.  2013.  Trophic omnivory across a productivity gradient:  intraguild predation theory and the structure and strength of species interactions.  Proceedings of the Royal Society Series B 280:.

J. D. Yeakel, M. Novak, P. R. Guimarães Jr, N. J. Dominy, P. L. Koch et al.  2011. Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions. PLoS ONE 6(7): e22015. doi:10.1371/journal.pone.0022015

M. Novak, J. T. Wootton, D. F. Doak, M. Emmerson, J. A. Estes, and M. T. Tinker.  2011.  Predicting community responses to perturbations in the face of imperfect knowledge and network complexity.  Ecology 92:836-846.

Novak, M.  2010.  Estimating interaction strengths in nature:  experimental support for an observational approach.  Ecology 91:2394-2405.

Novak, M., and J. T.  Wootton.  2010.  Using experimental indices to quantify the strength of species interactions.  Oikos Volume: 119:1057-1063.

Novak, M.  2010.  Estimating interaction strengths in nature:  experimental support for an observational approach.  Ecology 91:2394-2405.

Doak,D., J. Estes, B. Halpern, U. Jacob, D. R. Lindberg, J. Lovvorn, D. Monson, M. T. Tinker, T. Williams, J. T. Wootton, I. Carroll, M. Emmerson, F. Micheli, and M. Novak.  2008. Understanding and predicting ecological dynamics:  are major surprises inevitable? Ecology 89:952-961.

Novak, M., and J. T. Wootton.  2008. Estimating the nonlinear interaction strengths:  an observational method for species-rich food webs. Ecology 89:2083-2089.

Novak, M., J. D. Yeakel, A. E. Noble, D. F. Doak, M. Emmerson, J. A. Estes, U. Jacob, M. T. Tinker, and J. T. Wootton. In Press. Characterizing species interactions: What is the community matrix? Annual Review of Ecology, Evolution and Sytematics.


MICHAEL FITZSIMONS:  Michael was co-advised by Mike Miller at Argonne National Laboratory. Michael explored the determinants of diversity in mycorrhizal fungi and how these communities develop over time. His experiments focused particularly on feedbacks between plant and soil organisms, exploring whether negative or positive feed backs result from prolonged interactions and how that shapes succession. He combined his small scale experimental results with analyses of soil-plant interactions of the chronosequence of prairie restoration experiments at Fermi National Laboratory to evaluate how the short-term, small scale patterns play out over larger spatial and temporal scales.  Michael is now at the University of Chicago’s Center for Data Intensive Science.

Fitzsimons, M. S., and R. M. Miller.  2010.  The importance of soil microorganisms for maintaining diverse plant communities in tallgrass prairie.  American Journal of Botany 97:1937-1943.

Fitzsimons, M. S., and R. M. Miller.  2010.  Serpentine soil has little influence on the root-associated microbial community composition of the serpentine tolerant grass species Avenula sulcata.  Plant and Soil 330:393-405.

Fitzsimons, M. S., M. R. Miller, and J. D. Jastrow.  2008.  Scale-dependent niche axes of arbuscular mycorrhizal fungi.  Oecologia (Berlin) 158:117-127.


AARON KANDUR: Aaron studied the patterns and causes of range distributions, particularly the causes of sharp range edges and why they vary spatially. Intertidal species have unusually shaped ranges that are extremely long but very skinny, which facilitates studies of range determinants. Typically range boundaries are ascribed to single limiting factors, but these may not explain spatial variaton in range edges. Using censuses and experiments across a tidal gradient in conjunction with mechanistic and neural net modeling, Aaron investigated how multiple processes (production, physical stress, consumer performance, recruitment) change across strong gradients, and whether these factors can be linked to large-scale shifts in ranges, focusing on the mussel Mytilus californianus.


WILL TYBURCZY: Will investigated how differences in the temporal scale of different ecological processes (birth, death, growth, predation) affect the outcome of species interactions. For example, predator and prey births are often highly episodic annual events, whereas predator consumption of prey occurs fairly continuously through the year. He  developed models that integrate processes that operate on different time scales and carried out manipulations of snail predators and barnacle prey to estimate parameters and test model predictions.  Will is now a Program Analyst for NOAA.



KRISTEN JENKINS VOORHIES:  Kristen was co-advised by Sue Kidwell.  She used both ecological and palaeontological data to probe how environmental impacts such as climate change and wave energy harvesting impact community organization, and whether there are distinct differences in signals between human and non-human generated change.  Kristen is now working with the US Fish and Wildlife Service.



SEBASTIAN HEILPERN:  Sebastian studied the role of woody debris in tropical rivers and oxbow lakes at Cocha Cashew, Peru. The work exploring these structures in the context of being process catalysts, creating hotspots of production and changing food web interactions.  Sebastian is now at Columbia University.



SARA JACKREL Sara is studying how individual variation in terrestrial vegetation affects river communities through leaf litter fall.  Specifically, she is doing experiments testing whether individual trait variation in alders determines rates of decomposition in rivers, and exploring whether these traits determine susceptibility to terrestrial herbivores.  If so, then natural selection on and phenotypic plasticity of traits in one habitat can have cascading effects on the function of other ecosystems through material transport.  Sara is now at the University of Michigan.  Publications involving work done in part at the University of Chicago include:

Jackrel, S. L., and J. T. Wootton.  2014.  Local adaptation of stream communities to intraspecific variation in a terrestrial ecosystem subsidy.  Ecology 45:37-43.

Jackrel, S. L., and J. T. Wootton.  2015.  Cascading effects of induced terrestrial plant defences on aquatic and terrestrial ecosystem function. Proceedings of the Royal Society , Series B. 282: 20142522.

Jackrel, S. L., and J. T. Wootton. 2015. Diversity of riparian plants among and within species shapes river communities. PLoS ONE 10(11): e0142362.  doi:10.1371/journal.pone.0142362

Jackrel, S. L., T. C. Morton, and J. T. Wootton. 2016.  Intraspecific leaf chemistry drives locally accelerated ecosystem function in aquatic and terrestrial communities. Ecology 97: 97:2125-2135. doi: 10.1890/15-1763.1

Jackrel, S. L., S. M. Owens, J. A. Gilbert, and C. A. Pfister. In press. Identifying the plant associated microbiome across aquatic and terrestrial environments:  the effects of amplification method on taxa discovery.  Molecular Ecology Resources.


ELIZABETH SANDER:  Liz was co-advised by Stefano Allesina.  She is developing network theory and analysis that can be connected to the interaction web data from Tatoosh Island, Washington that has been collected over the past 45 years.  This includes developing realistic interaction web models to test for commonalities in behavior with patterns observed in empirical webs, developing algorithms to fit time series data to multi-species models, testing methods to infer network structure and causal inference from time series data, and probing for structural patterns in the Tatoosh interaction web. Lis has taken a position at Civis Analytics.

Allesina, S. E. Sander, M. J. Smith, and S. Tang.  2013.  Superelliptical laws for complex networks.  arXiv preprint arXiv:1309.7275

Sander, E. L., J. T. Wootton, and S. Allesina.  2015.  What can interaction webs tell us about species roles? PLoS Computational Biology. 11(7): e1004330. doi:10.1371/journal.pcbi.1004330

Smith, M. J., E. Sander, G. Barabás, and S. Allesina.  2015.  Stability and feedback levels in food webs.  Ecology Letters 18: 593-595.