Theoretical Ecology Lab Tea


The Theoretical Ecology Lab Teas are informal meetings where members of affiliated lab groups give talks on their current research and receive feedback from their audience.  The talks are 30 minutes and are scheduled on Wednesdays at 12.30pm in Eno Hall 209.

Talk schedules and email lists are maintained by Carey Nadell, Liliana Salvador and Sarah Batterman. Please contact , or to have your name added to the labtea email list so that you can receive reminders about upcoming lab teas.


Fall 2009

Wednesday September 16th at 12.30pm Simon Leblanc (ENSEIRB MATMECA BORDEAUX, France)
Wednesday September 23th at 12.30pm Ryan Chisholm
Wednesday September 30th at 12.30pm Vishwesha Guttal
Wednesday October 7th at 12.30pm Petra Klepac
Special LabTea: Monday October 12th at 12.30pm Francisco Dionisio (Universidade de Lisboa, Portugal)
Wednesday October 14th at 12.30pm Miguel A. Fortuna
Wednesday October 21st at 12.30pm Jeremy Lichstein
Wednesday October 28th at 12.30pm Virginia Pitzer
Special LabTea: Friday November 6th at 12.30pm Adi Livnat (Berkley University, USA)
Wednesday November 11th at 12.30pm Erik Osnas
Wednesday November 18th at 12.30pm Adrian de Froment
Special LabTea:Thursday November 19th at 12.30pm in Guyot Hall 100 Tom Butler
Wednesday November 25th at 1.30pm Michael Raghib
Wednesday December 2nd at 12.30pm Liliana Salvador
Wednesday December 9th at 12.30pm Ray Dybzinski
Wednesday December 16th at 1.30pm Carey Nadell

Titles and abstracts

Wednesday September 16th at 12.30pm

Exploring phase transitions and collective behavior in animal groups using novel imaging techniques.
Simon Leblanc
To explore collective behavior in animal groups, experiments on fish schools have been done in the Couzin Lab. They produced a lot of data to analyze. When the group size is small enough, it is possible to track individuals and get their trajectories. This provides very precise information at a very fine level. Unfortunately, these methods loose accuracy when the group size increases, and it is impossible right now to track more than 300 individuals. However, it is crucial to be able to make measurements for larger group size. I will present in this Lab Tea a method based on optical flow estimation for extracting the velocity field, density and alignment of the fish at a coarse level, which has been successful for analyzing groups of 1000 fish, and which we can apply even on larger groups. I will also present some preliminary results about phase transitions and correlation length.

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Wednesday September 23rd at 12.30pm

Assigning biological meaning to the parameters of the neutral theory of biodiversity promotes rigorous confrontation with data.
Ryan Chisholm

A key goal of community ecology is to understand the mechanisms that generate observed global patterns of biodiversity. To achieve this, we require theoretical mechanistic models based on biologically meaningful parameters such as dispersal distances and speciation rates. I will report on our recent successful attempt to relate the heretofore mysterious immigration paper of Hubbell's spatially implicit neutral theory to the parameters of a dispersal kernel and the geometry of the plot defining the community. I will demonstrate three benefits of this work. Firstly, I will show how the immigration parameter can now be estimated independently from dispersal data rather than treated as a free fitting parameter, and I will compare these new independent estimates with previous fitted values. Secondly, I will show how the result can be used to make new predictions about species-abundance distributions and species-area curves and I will compare these predictions to tropical forest data. Thirdly, I will discuss how the results can be used to assess the errors in the mean field approximations associated with the spatially implicit models. This work is an important step towards promoting rigorous confrontation of the neutral theory with data and thereby facilitating comparison with competing models such as niche theories.

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Wednesday September 30th at 12.30pm

Animal mediated long distance dispersal of seeds.
Vishwesha Guttal

Empirical studies suggest that the dispersal of seeds to large distances can occur much more frequently than a Gaussian kernel would predict. Such `fat-tailed' long distance dispersal (LDD) is predicted to have disproportionate impact on population and community dynamics. Animals form a key biotic vector of seeds and pathogens, but very little is known about the influence of individual animal behavior that drives LDD. I present a simple analytical model that links individual animal behavior with large scale patterns of LDD and makes testable predictions. This work was done when I was a graduate student (during a summer school) and in a field am not too familiar with. I am looking forward to receiving feedback at LabTea.

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Wednesday October 7th at 12.30pm

Optimizing reactive responses to outbreaks of immunizing infections - case management vs vaccination.
Petra Klepac

When controlling outbreaks of infectious diseases, the two most common approaches are treatment of infectious cases and mass vaccination campaigns. We formulate a SEIR model that includes those two control strategies - palliative care and vaccination. Using mostly numerical techniques, we investigate a range of strategies we can implement after the epidemic has started and try to find a rule-of-thumb principle for control of outbreaks.

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Monday October 12th at 12.30pm

Spiteful and Selfish Behavior through biological warfare.
Francisco Dionisio (Universidade de Lisboa, Portugal)

Biological warfare, also known as a germ warfare or biological weapons, is the use of any pathogen or parasite as a means of harming other individuals. Can individuals use their pathogens/parasites as biological weapons to harm other individuals? That is, use pathogens as spiteful or selfish agents? In this seminar, I discuss the likelihood of this hypothesis.

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Wednesday October 14th at 12.30pm

Spatial Networks in Ecology // Coevolution in Networks of Interacting Species.
Miguel A. Fortuna

In this talk I would like to present very briefly what I have done during my PhD so that you can know my previous work, and also what I am going to do at Princeton during my postdoc in order to receive feedback. In the first part of the talk I will show you how the framework of complex networks (webs consisting on a set of nodes connected by links) is a useful approach to understand how biodiversity is organized at different scales. Specifically, I have identified the spatial scale of ecological processes such as dispersal and migration in fragmented landscapes, behavioral processes such as social structures in animals, and evolutionary processes such as gene flow in plant populations. In the second part of the talk I will introduce the mathematical approaches to the study of coevolution, that is, reciprocal evolutionary change between interacting species driven by natural selection. The question to be explored is to what extent the coevolutionary process shapes the architecture of ecological networks of interacting species such as food webs and plant-animal mutualistic networks.

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Wednesday October 21st at 12.30pm

Tree coexistence in a forest metacommunity
Jeremy Lichstein

The factors that control tree coexistence, and thus diversity, are still poorly understood. The recently developed quasi-realistic, yet tractable, perfect plasticity approximation (PPA) forest model is a tool that can potentially provide some answers. I will discuss a metacommunity version of the model, in which trees coexist via successional and edaphic (soil-related) tradeoffs. An analytical approximation for the late successional equilibrium (i.e., a forest that has not been disturbed for a very long time) suggests that even slight edaphic specialization results in the locally dominant species occupying nearly the entire habitat. However, the transient dynamics are slow, so that single-species dominance is rarely observed. The competitive dynamics between late-successional species are qualitatively similar in the presence or absence of early-successional species. The results suggests that source-sink dynamics may be an important factor contributing to local (alpha) tree diversity.

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Wednesday October 28th at 12.30pm

Effects of demography and vaccination on the spatiotemporal dynamics of rotavirus epidemics in the United States and beyond.
Virginia Pitzer

The seasonal geographical spread of rotavirus in the United States has been a hitherto mysterious pattern. Rotavirus epidemics have historically begun in the southwest, where epidemics peaked in December-January, and spread towards the northeast, where epidemics peaked in March-April. In recent years, however, this trend has diminished as epidemics have been occurring later in southwestern states. Standard explanations such as traveling waves or environmental drivers cannot account for these patterns. Using a mathematical model of rotavirus transmission calibrated against state-specific data on disease incidence, we show that spatiotemporal variations in U.S. birth rates can explain the apparent traveling wave of epidemics. The recent large-scale introduction of rotavirus vaccination provides a means of validating our model predictions. Allowing for this artificial reduction in susceptible recruitment generates a predicted pattern of reduced and lagged epidemics closely matching the observed response to vaccination. Armed with this validated model, we explore the relative importance of direct and indirect (herd immunity) protection, a key issue in determining the worldwide benefits of vaccination.

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Wednesday November 11th at 12:30pm

Adaptive Dynamics of Virulence: Mycoplasma conjuctivitsis in House Finch Populations and Communities
Erik Osnas

I will present some preliminary theoretical results on virulence evolution when disease transmission occurs before major disease mortality or morbidity in single and two-species host communities. My work is motivated by lab and field data collected by collaborators on Mycoplasma gallisepticum (MG) infecting House Finch, American Goldfinch, and other bird populations across the United States. We have exciting new results consistent with geographic variation in virulence evolution during the emergence of this disease. I would welcome any feedback on our interpretation of these empirical results and on my models of virulence evolution.

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Wednesday November 18th at 12:30pm

A Hidden Dimension to Decision Making: Animals Balance Speed, Effort and Accuracy
Adrian de Froment

All animals need to make the best decisions possible in order to maximize their Darwinian fitness. A widespread view in biology is that animals face a simple trade-off between speed and accuracy, which they balance according to the costs and benefits involved. For example, a swarm of bees will spend less time choosing a new nest site if the cost of remaining in the open increases, at the same time accepting a higher chance of choosing a suboptimal home. However this picture ignores a third dimension to the trade-off: animals can also vary the effort per-unit-time that they invest in reducing their uncertainty about their options. This is important because the costs of time and effort can vary independently. Using a standard model of decision-making, I examine whether perfectly adapted animals should make use of this to improve their decision-making. I compare individuals who can adjust both the time and the effort they invested in a decision with a second group who can adjust only the time. As the cost of time rises, the animals in the both scenarios make quicker decisions, but those in the first group also increase their level of effort, and so are able to maintain a higher level of accuracy. The model makes testable predictions about how this three-way trade-off between speed, effort and accuracy should manifest itself in nature. This will be important to researchers interested in decision-making in biology and neuroscience.

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Thursday November 19th at 12:30pm in Guyot Hall 100

Robust ecological pattern formation induced by demographic noise
Tom Butler

We demonstrate that demographic noise can induce persistent spatial pattern formation and temporal oscillations in a simple model due to Levin and Segel of predator-prey model for plankton-herbivore population dynamics. Although the model exhibits a Turing instability in mean field theory, demographic noise greatly enlarges the region of parameter space where pattern formation occurs. To distinguish between patterns generated by fluctuations and those present at the mean field level in real ecosystems, we calculate the power spectrum in the noise-driven case and predict the presence of fat tails not present in the mean field case. These results may help account for the prevalence of large-scale ecological patterns, beyond that expected from traditional non-stochastic approaches.

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Wednesday November 25th at 12:30pm

Multiscale, adaptive representations of microbial community structure and biogeochemical cycles in the oceans
Michael Raghib

The development of predictive models of microbial community composition in the oceans for various regimes of disturbance and nutrient availability is central to our understanding of how these communities drive, and respond to, global biogeochemical cycles. Progress has been hampered by three major difficulties. First, experimental and field information about the relative distribution of biogeochemically relevant metabolic functions and trade--offs is limited to a handful of organisms that can be cultured; although new cultivation techniques, together with environmental genetic sequencing (i.e. metagenomics) seem promising, significant challenges remain. The second problem is theoretical. How should one construct a model that is capable of adaptation, in the sense that types that occur at low abundances under some environmental conditions, discarded in traditional aggregated models, are allowed to become dominant when the right conditions prevail? Third, experiments typically target fully mixed environments, but fluid environments in the oceans are highly structured (layers, turbulent eddies). My current research targets these problems by developing computational experiments based on an algal cell IBM for the first case , flexible, trait based representations of community composition in the second, and variants of fractional kinetics in the third.
Work in progress, in collaboration with S. Dutkiewicz (MIT), M. Follows (MIT), John Dunne (GFDL), Charlie Stock(GFDL), Juan Bonachela (Levin Lab) and S. Levin

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Wednesday December 2nd at 12:30pm

Efficient stochastic searches and methods to analyze 'worm' movement behaviors
Liliana Salvador

The study of animal foraging behavior has extreme importance in the field of ecology and exemplifies the wider scientific problem of optimizing search strategies. There is empirical evidence that the type of searching strategies employed by animals while foraging (systematic or random) depends on the amount of information that is involved in the search process. When information is lacking, the random search is a possible strategy. In this case, an important question to ask is what statistical strategy will be the most efficient to find food? To be able to answer it, it is important to know which are the behavioral mechanisms that allow animals to perform efficient stochastic searches. During labtea, I will be focusing on the behavior mechanisms that the nematode C. Elegans use during its searching process and on the methods to automatically identify these mechanisms.

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Wednesday December 9th at 12:30pm

Leaf longevity: understanding community-level patterns in forests by scaling-up individual-level physiology in the context of light and nitrogen competition
Ray Dybzinski

Leaf life spans of forest trees range from a few months to nearly a decade. Three generally accepted relationships pertain to any explanation of this conspicuous fact: Compared to shorter-lived leaves, longer-lived leaves are... (1) thicker, with lower maximum rates of photosynthesis; (2) more nitrogen-use-efficient because the nitrogen used to build each leaf is retained for longer; and (3) slower to decompose. Innumerable verbal arguments and a few models have integrated these facts to explain observed patterns, but none of them take a whole-plant, community-level perspective and none are quantitative. The Pacala Lab’s PPA model of height-structured light competition is an ideal modeling framework to fill this void (and I do hereby swear that my review of it will be brief). I may have some results by Wednesday, but my main goal for this Lab Tea is to lay out the problem and our proposed approach in the hope that you can help identify profitable routes we hadn’t considered or demons to avoid.

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Wednesday December 16th at 1:30pm

A fairly simple model of the evolution of bacterial quorum sensing
Carey Nadell

Many bacteria possess quorum-sensing (QS) systems that are thought to detect population density in the local environment. They accomplish this by secreting small signal molecules, monitoring their concentration with specialized receptors, and adjusting their behavior in response to changes in signal abundance. Numerous phenotypes fall under QS control, including basic metabolic activity, sporulation, competence (the ability to take up extracellular DNA and incorporate it into one's own genome), surface attachment, biofilm formation, and the secretion of digestive enzymes and many other molecules. QS is a type of social behavior at heart, and social evolutionists have shown great interest in exploring it theoretically and empirically. However, their analyses often do not distinguish between the QS regulatory mechanism and the phenotypes that it regulates. They also tend only to consider a small subset of QS-regulated phenotypes: cooperative public goods like extracellular enzymes. My goal is here is to start simpler, thinking about why and when quorum sensing provides a net benefit as a buffer against environmental uncertainty.

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Links to previous schedules

    Fall 2000    Spring 2001
    Fall 2001    Spring 2002
    Fall 2002    Spring 2003
    Fall 2003    Spring 2004
    Fall 2004    Spring 2005
    Fall 2005    Spring 2007
    Fall 2007    Spring 2008
    Fall 2008    Spring 2009   

Last update: 25th September 2009