Yue (Max) Li
Friends of the Lab
Our study systems
Some of us are fond of studying communities of
annual plants. We find these in the deserts of Arizona and Eyre
(South Australia), in the vernal pools of the Central Valley of
and in the coastal
swales near Bodega Bay. We also study
perennial herbs in the
understorey of Eucalypt forests in Australia. Some of us
are aquatic in orientation studying aquatic insects and amphibia in
ponds and streams, or invertebrates in
There are lots of systems that we think about
but do not collect data on ourselves, at least not right now. These
reef fish communities, tropical forests, and host-parasitoid systems.
For studies of natural systems, we are developing new classes of quantitative tools to test coexistence mechanisms and hypotheses about dynamics of populations and communities subject to spatial and temporal variation. Then we go out into the field to count, measure, and manipulate.
For theoretical studies, we use math and
computers. We are fond
of probability and statistical theory. We also get into
and Fourier transforms.
and its maintenance
testable community theory
Classification of Ecological Variation
dynamics in time and space
Natural communities inhabitat a world of great complexity in time and space. The physical environment has many spatial complexities in its topography, hydrology and soils. And it changes over time: organisms experience varying weather and climatic changes on many scales interacting in a variety of ways with spatial environmental varation. Various processes, not just the physical environment, but also interactions between organisms, cause their densities to vary greatly in space and time too. It has often been hypothesized that these different kinds of variation have important roles in diversity maintenance. But what are those roles? Development of mathematical models with such complexities is not easy, and so it is perhaps not surprising that much mathematical theory, even if it addresses density variation in time or space, rarely includes variation in the physical environment. The theory coming from this lab is different. We have embraced environmental complexity, and gathered the mathematical tools necessary to study it. The result is a comprehensive multiscaled theory of diversity maintenance that includes the standard equilibrium theory as a special case. This work has led to the recognition of several new species coexistence mechanisms including the storage effect, nonlinear competitive variance, and fitness-density covariance.
Multitrophic diversity maintenance
The study of diversity maintenance mechanisms has traditionally focused on competition, with predation mostly seen as modifying what competition does. However, there is growing evidence that predation and competition can have very similar effects on the maintenance of species diversity. This similarity of action relies on the observation by Bob Holt (University of Florida) that both predation and competition can lead to mutually negative indirect interactions between species. Of most importance, such mutually negative indirect interactions apply not just between species but also to different individuals within the same species. Theoretical consequences of these facts mean that predation and competition each have the potential to limit diversity or promote diversity. For both predation and competition it all depends on the extent to which within species interactions outway between species interactions. When predation and competition have similar strengths for a given set of interacting species, the overall outcome for diversity
represent a compromise between the separate tendencies of predation and
competition in the given circumstances. In other cases, new mechanisms
promoting diversity arise from the interaction between predation and
competiton. If one mechanism is much stronger than the other, the
tendency of the stronger mechanism prevails.
How do species coexistence mechanisms work? And how do we know how strong they are? Our lab has developed measures of mechanism strength based on how much a mechanism increases the rate of recovery of a species from low density. In nature, species always fluctuate, and if they are to remain in a community, they must recover from their low excursions. Focusing on these recovery rates, we have found ways of quantifying mechanism strength in terms of the
functional components that define the mechanism. This has led not only to a big increase in understanding of mechanism functioning, but also powerful new ways of testing mechanisms.
mechanisms, mulitple scales
Community Processes in Variable Environments
The natural world is inherently variable. The
physical environment varies on all scales and so do the organisms
inhabiting it. Organisms
are adapted to this variability, not merely hedging against uncertainty
taking advantage of opportunities that variability brings. My main
interest is how the adaptation of organisms to variability promotes
species diversity and affects ecosystem functioning. I do this
primarily theoretically by developing
mathematical models using probability theory and the methods of
statistics. Recent research topics have involved neighborhood
models, community assembly, invasion resistance, multitrophic diversity
maintenance, life-history theory and the various
of temporal and spatial niches, also known as the storage effect and
nonlinearity of competiton. In addition, I am involved with field
on annual plants and herbaceous perennial plants. Other systems that
foci of theorizing are coral reef communities, tropical forests, and
in mediterranean climates.
Some recent publications
P. 2000. Mechanisms of maintenance of species diversity. Annual Review
of Ecology and Systematics 31, 343-66.
P. 2000. General theory of competitive coexistence in spatially varying
environments. Theoretical Population Biology 58, 211-237.
Chesson, P. 2001.
Metapopulations. Pp 161-176 in Encyclopedia of
Biodiversity, Vol 4, Simon A. Levin, ed, Academic Press.
K., Chesson, P. 2002. Community ecology theory as a framework for
biological invasions. Trends in Ecology and Evolution 17, 170-176.
Chesson, P., Peterson, A.G. 2002. The quantitative assessment of the benefits of physiological integration in clonal plants. Evolutionary Ecology Research 4, 1153–1176.
P. 2003. Quantifying and testing coexistence mechanisms arising from
recruitment fluctuations. Theoretical Population Biology 64,
P., Gebauer, R. L. E., Schwinning, S., Huntly, N., Wiegand, K.,
Ernest, S. K. M., Sher, A., Novoplansky, A., and Weltzin,
J.F. 2004. Resource pulses, species interactions and diversity
maintenance in arid and semi-arid environments. Oecologia 141,
236 - 253.
Facelli, J.M., Chesson, P., Barnes, N. 2005. Differences in seed biology of annual plants in arid lands: a key ingredient of the storage effect. Ecology 86, 2998-3006.
P., and Lee, C.T. 2005. Families of discrete kernels for modeling
dispersal. Theoretical Population Biology 67, 241-256.
P., Donahue, M., Melbourne, B., Sears, A. 2005. Scale
transition theory for understanding mechanisms in
metacommunities. In Holyoak, M, Leibold, M.A., Holt, R.D., eds,
Metacommunities: spatial dynamics and ecological communities, pp
A.L.W., Chesson, P. 2007. New methods for quantifying the
spatial storage effect: an illustration with desert annuals.
Ecology 88, 2240-2247
P. 2008. Quantifying and testing species coexistence
mechanisms. Pp 119 – 164 in Valladares, F., Camacho, A., Elosegui, A.,
Estrada, M., Gracia, C., Senar, J.C., & Gili, J.M., ed. “Unity in
Diversity: Reflections on Ecology after the Legacy of Ramon Margalef.”
Communities in varying environments
Coexistence in a temporally varying environment is
predicted to arise when species differ in their temporal patterns of
resource consumption. However, key to this outcome is coupling of
resource consumption and resource availability. High resource
consumption rates, due to favorable environmental conditions, are
expected to draw down resources, causing high competition. The
phenomenon is called covariance between environment and competition
(covEC). For coexistence to occur, covEC must be weaker for a species
perturbed to low density (an “invader”) compared to an unperturbed
species (a “resident”). However, these outcomes have not been
thoroughly investigated in models. Instead, the formulation of
models often implicitly includes them. Thus, the theory is
incomplete because there is no satisfactory theory of this key
component, covEC. Moreover, it has been suggested detecting covEC in
nature provides a powerful means of testing coexistence by the storage
effect. The phenomenon of covEC therefore requires a thorough
theoretical understanding. Here we extend the MacArthur
consumer-resource model to varying environments. The explicit
resource dynamics in the MacArthur model allow a theory of covEC to be
developed. Our approach was to develop quantitative measures of factors
contributing to covEC, and studying their effects in computer
simulations. We found that relative speeds of resource
dynamics and environmental variation have major effects on covEC.
Resource speed by far had the dominant effect and can be divided into
two major components, resource amplitude, and resource phase relative
to consumers. Resident covEC is maximal when resource amplitude
is greatest and phase relative consumers is zero, and this is achieved
when resources turn over rapidly, most strongly promoting coexistence
by the storage effect. These results allow us to address the
fundamental ideas of Hutchinson’s Paradox of the Plankton. While
they do show that seasonal environmental variation can promote
coexistence of consumers on limited resources, it produces very
different predictions about time scales of environmental change and
consumer dynamics compared with Hutchinson. Contrary to
Hutchinson’s predictions we find that slow consumer dynamics are
favorable to coexistence and do not lead to averaging of environment
fluctuations, nullifying their effects. Critical to coexistence is
factors strengthening covEC for residents, found here to be fast
resource dynamics, not intermediate consumer dynamics.
Species-specific germination speed and coexistence in a desert annual plant community. Desert annual pants are frequently the subjects of coexistence studies with a focus on the role of environmental variation. Germination rates are observed to vary substantially over time forming the basis of the storage-effect coexistence mechanism. Laboratory germination studies have reproduced some of this variation, but do not replicate the full range of conditions found in the field. Here we discuss one aspect of field variation that potentially has a major effect on plant species coexistence, but has been neglected in the past. Experimental and observational data from the desert annual plants at our field site near Portal, AZ show distinct species-specific differences in the speed of germination following rainfall. This indicates an important and previously unexplored opportunity for covariance between competition and the environment, a key quantity for coexistence by the storage effect. Most seeds are at or near the surface, and so moisture at the soil surface is critical for germination. Duration of this moisture varies greatly due to duration, and spacing of rainfall events, and also due to solar radiation, temperature, humidity and wind following these events. Field observations and laboratory experiments show that the observed differential germination speed is strong enough to lead to different species dominating due to different durations of soil moisture. Thus, variation in duration of surface soil moisture potentially contributes substantially yearly variation in the species composition of the annual plant community. Using data on germination speed from field observations and germination experiments in the lab, we built a model linking fluctuations in surface soil moisture and species’ germination speeds to predict the crop of plants resulting from specific rainfall patterns. Our model implies that the interaction of species-specific germination speed with variation in soil moisture makes a major contribution to the storage-effect coexistence mechanism in this community. For example, species that germinate quickly have greater opportunity to take advantage of short-duration rainfall and surface soil moisture, while other species require a longer period of surface soil moisture to successfully germinate, but may be superior competitors once germinated. Incorporating the interaction between germination speed and the duration and spacing of rainfall greatly expands the opportunities for species coexistence in this community. This increased understanding of the factors controlling community composition also provides a more refined understanding of the long-term stability of species composition.
Yue (Max) Li
Physiological Ecology of Plant Invasions
I am studying the causes of the dramatic
irruption of the Eurasian invasive plant, Erodium cicutarium, in the San
Simon Valley of southeastern Arizona. It many areas, it is now
95% or more of
the winter annual plant biomass, up from a miniscule
presence away from roads in the 1980s. At the same time, native
winter annual plants have become very rare and are showing changes in
species composition. This new monoculture potentially has
profound implications for biodiversity, habitat quality, ecosystem
functioning and forage quality of the rangeland. My research applies a
physiological, ecosystem, community and theoretical approach to
understanding the characteristics associated with the irruption and
distribution of E. cicutarium
and its impacts for biodiversity in the San Simon Valley.
Non-equilibrium dynamics and species coexistence
Non-equilibrium dynamics of natural ecosystems have a major role in generating and maintaining biodiversity. The main objective of my research is the mechanistic understanding of this role in both ecological and evolutionary context. In particular I am interested in life history evolution with frequency dependent selection in temporally fluctuating and spatially heterogeneous environments.
Maureen RyanEnvironmental variation and species interactions in amphibian communities
I'm interested in how environmental variation promotes diversity within species and communities, and how mechanisms such as the storage effect that function through environmental variation can affect endangered species, in particular. My research focuses on a grassland salamander community in the Central Valley of California that includes the threatened California tiger salamander (Ambystoma californiense), hybrid tiger salamanders (A. californiense crossed with A. tigrinum mavortium, an introduced tiger salamander from the central US), and the California newt (Taricha torosa).
I'm using a combination of artificial pond experiments and field experiments to look at whether and how environmental variation promotes coexistence between the two native species, Ambystoma californiense and Taricha torosa, and how coexistence mechanisms operating in the native community are influenced by the addition of hybrid salamanders. Additionally, I'm looking at how environmental variation influences hybridization dynamics between A. californiense and A. tigrinum mavortium and whether mechanisms associated with environmental variation can contribute to the maintenance of genetic polymorphism within hybridizing populations of tiger salamanders. Besides experiments, I'm using theoretical modeling and data from field surveys/sampling to investigate how dispersal and landscape structure interact with local community dynamics to influence species diversity and hybrid spread on a regional scale.
From a conservation perspective, my work is motivated by an interest in how landscape alteration may influence amphibian diversity and species coexistence within extant communities, and in particular how common pond manipulations and the loss of vernal pools in the California Central Valley might influence California tiger salamander populations.
Environmental variation and species interactions
Ecology is challenged to find simple ways to understand the messiness of the natural world. I like to work from a metacommunity context, accepting that natural ecosystems contain a variety of different habitat types, and that this environmental variation affects the interactions of species within ecosystems. My PhD research specifically involves using natural annual plant systems to test how variation in the environment affects species coexistence. I am also interested in how environmental variation affects food-web interactions, and generally interacts with other forms of density dependence. My field sites are in the Chihuahuan desert and at the Bodega Marine Reserve.
Scale dependence in marine populations
For my dissertation research, I studied how spatial variation in local density-dependent processes influences regional dynamics. In collaboration with Marcel Holyoak, I investigated the effects of local resource distribution, dispersal rate, and the strength of density dependence on regional dynamics in a highly manipulable microcosm system, in which we could track population dynamics over time. Applying the same principles to a field system, I studied Petrolisthes cinctipes, a filter-feeding porcelain crab that lives in intertidal cobblefields along the Pacific coast. Based out of Bodega Marine Laboratory, I parameterized models of local density-dependence in this organism using field and laboratory experiments. For Petrolisthes cinctipes, the primary sources of density dependence are gregarious settlement, competition, and predation. With Leah Akins, I quantified the spatial variation that influences these process at two scales: variation in P. cinctipes density, predator abundance, and larval supply among rocks within sites and among sites. By integrating information about spatial variation into empirically-based models of local dynamics, we can predict what local processes are most important when "scaling up" to regional dynamics. For links to publications and Megan's CV, see her website.
Population dynamics and spatial heterogeneity
My main research interest is population dynamics, especially how small-scale heterogeneity affects dynamics at larger scales. Understanding how spatial and temporal heterogeneity affect the dynamics of populations and communities is fundamental to ecology. Indeed, answers to the most prominent questions in ecology involve the pervasive influence of heterogeneity. Why do species coexist? Why are there so many species? Why do some species cycle whereas others don't? How does habitat fragmentation affect extinction? Why are some species more invasive than others? Spatial and temporal variation in population densities and in the physical environment are essential considerations in these questions. My current research and research to date focuses on the effects of spatial heterogeneity. Whereas empirical studies have typically focused on heterogeneity exclusively, theory demonstrates that population dynamics are altered by spatial heterogeneity only when heterogeneity interacts with nonlinear demographic processes - the pillar for research in the Chesson lab. The aim of my research is to develop empirical tools to measure the interaction of nonlinearity and heterogeneity and to use these tools to probe real populations. Thus, I tackle the important issue of how to integrate theory and models with data from real systems, to understand how the interaction of spatial heterogeneity and nonlinearity alters population dynamics. I use these insights to address important basic and applied questions in ecology.
The persistence of species in patchy landscapes
My research focuses on testing and refining theory that makes predictions about the persistence of species in heterogeneous landscapes, including metapopulation and related spatio-temporal theory. So far, I have concentrated on the spatial and temporal dynamics of populations and communities in landscapes that have been modified by humans, through habitat fragmentation and grazing. I am interested in how the life history characteristics of species determine the response of species to landscape heterogeneity. I use quantitative methods to test theory and have approached this work using data from a large-scale, long-term field experiment for beetles and data for a continental scale study of arid zone birds in Australia.
I am currently broadening this focus to explore what this same theory predicts about patterns of biological diversity in naturally patchy landscapes. I am focusing on the grassland plant community in serpentine patches in a non-serpentine matrix (in the University of California’s McLaughlin Reserve). Right now, I am particularly interested in spatial scale and the relationship between diversity and invasibility (Shea and Chesson 2002).
Shea, K., Chesson, P. 2002. Community ecology theory as a framework for biological invasions. Trends in Ecology and Evolution 17, 170-176.
Some recent publications
Davies, K.F., Chesson, P., Harrison, S., Inouye, B.D., Melbourne, B.A., Rice, K.J. 2005. Spatial heterogeneity explains the scale dependence of the native-exotic diversity relationship. Ecology 86, 1602-1610.
Davies, K. F., C. R. Margules, and J. F. Lawrence. 2004. A synergistic effect puts rare, specialized species at greater risk of extinction. Ecology 85: 265-271.
Davies, K. F., B. A. Melbourne, C. R. Margules, and J. F. Lawrence (in press). Metacommunity structure influences the stability of local beetle communities. In M. Holyoak, M. A. Leibold and R. D. Holt eds. Metacommunities: Spatial Dynamics and Ecological Communities. Chicago, University of Chicago Press.
Davies, K. F., B. A. Melbourne, and C. R. Margules. 2001. Effects of within- and between-patch processes on community dynamics in a fragmentation experiment. Ecology 82: 1830-1846.
Davies, K. F., C. Gascon, and C. R. Margules. 2001. Habitat Fragmentation: consequences, management and future research priorities. Pages 81-97 in M. E. Soulé and G. H. Orians, editors. Conservation Biology: Research Priorities for the Next Decade. Island Press, Washington.
Davies, K. F., C. R. Margules, and J. F. Lawrence. 2000. Which traits of species predict population declines in experimental forest fragments? Ecology 81: 1450-1461.
Davies, K. F., and C. R. Margules. 1998. Effects of habitat fragmentation on carabid beetles: experimental evidence. Journal of Animal Ecology 67: 460-471.
Theory of multispecies interactions; human-environment interactions
I study the theory of multispecies interactions, with specific focus on the matrix of coefficients for all pairwise interactions in a community. Specific projects include: 1) Determining relationships between different patterns of direct and indirect competitive (or facilitative) interactions and the structure of model community matrices; 2) determining patterns of shared resource use that result in specific community matrices; and 3) developing techniques to do 1) and 2). I also study human-environment interactions using theory from ecosystem ecology and demography.
Diversity maintenance in tropical plant communities
Diversity maintenance and nonlinear dynamics