Spring 2012

Titles and abstracts

Wednesday February 8th at 12:30pm

The Evolution of Intermittent Breeding
Allison Shaw
A central issue in life history theory is how organisms trade-off current and future reproduction. A variety of animals exhibit intermittent breeding, meaning sexually mature adults will skip breeding opportunities in between reproduction attempts. It's thought that intermittent breeding occurs when reproduction incurs an extra cost in terms of survival, energy, or recovery time. In this talk I'll present a matrix population model that I have developed for intermittent breeding, where I use adaptive dynamics to determine the evolutionarily stable strategy (ESS) for breeding frequency. In a constant environment there is a pure ESS, however environmental stochasticity can select for a mixed ESS. Finally, I'll discuss model results in the context of various species with intermittent breeding (e.g. reptiles, fish, sea birds).

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Wednesday February 15th at 12:30pm

Inferring community ecology from time-course metagenomic data
Alex Washburne
Data has arrived from another planet! Unfortunately, we lost the exhaustive data on species' traits and natural histories after somebody spilled bacon grease on the thumb drive and left it within reach of my dog (double whammy). I'm afraid all that's left is a very detailed time-course dataset on all the species in a community and their relative abundances. What can we do with this dataset? This seems like science fiction (or some pathetic attempt at it), but it's a problem we're faced with in microbial ecology with the surge of metagenomic data. The vast majority of microbes can't be cultured, but we can get at their relative abundances by the sequencing of conserved genes (e.g. 16s RNA). For this lab tea, I want to know what you all, as practicing ecologists, would do with this dream dataset; if you had species lists and relative abundances over time, how would you look at or analyze the data to make inferences about the underlying community ecology? I will provide a brief background of the context in which I'm studying this problem (neutral theory & the gut microbiome), and then I will try to facilitate collective thinking as we brainstorm what could be done with this ideal dataset.

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Wednesday February 22nd at 12:30pm

Not-so-great expectations for species range shifts? Thoughts on developing appropriate null models
Malin Pinsky
As the global climate warms, substantial attention is now focused on understanding whether, or rather, which, species will be able to shift their distributions and survive. Distribution shifts across a wide variety of species on land and in the ocean have already been observed, but there has been consistently large variation in rate and even direction of shift among species. Attempts to explain this variation have often failed, but we haven't paused to ask how much variation is simply random chance. Put another way, how much shift would we expect from a null model? I'll present some initial thinking about how we can answer this using branching random walks and matrix modeling, with a focus on the effects of stochastic dispersal. I'll also present simulations to include realistic fluid dynamics appropriate for a particularly stochastic environment, the coastal ocean, and would love your thoughts on further extensions and refinements.

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Wednesday February 29th at 12:30pm

Stochastic connectivity in marine metapopulations: causes and consequences.
James Watson
The probability of dispersal from one habitat patch to another is a crucial quantity in our efforts to understand and predict the dynamics of natural populations. Unfortunately, an often overlooked property of this potential connectivity is that it may change with time. For example, transient landscape features in marine systems, such as mesoscale eddies and along-shore jets, produce potential connectivity that is highly variable in time. Here, I will talk about the impact of this temporal variability by comparing simulations of nearshore metapopulations dynamics when potential connectivity is constant through time (i.e. when it deterministic) and when it varies in time (i.e. when it is stochastic). I use mathematical analysis to reach general conclusions and realistic biophysical modeling to determine the actual magnitude of these changes for a specific system - nearshore marine species in the Southern California Bight. I'll also discuss the influence of time-varying connectivity on the coexistence nearshore species, and I'd like to get your advice on whether this system can be examined through the lens of Adaptive Dynamics.

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Thursday March 1st at 4:00pm

The Intermediate Disturbance Hypothesis: Do We Still Care?
Meredith Root-Bernstein
Small mammals' effects on ecosystems have been widely studied. In articular, small mammal disturbance (grazing and biopedturbation) effects on plant communities have been researched in many species, and could be developed for use as natural agents of habitat restoration in some cases. While there are some hypotheses relevant to understanding how small mammal disturbances should increase plant richness and diversity, they are generally too underspecified to yield testable predictions, and are applied a posteriori if at all. Here I summarize and clarify how three similar and relevant hypotheses, the Intermediate Disturbance Hypothesis, the ecosystem engineering hypothesis applied to small mammal disturbances, and the perturbation hypothesis, interact. I produce a more explicit summary model, and I show how I tested aspects of it with the degu, Octodon degus, for my thesis. I discuss the further challenges to making the model more insight- and prediction-generating.

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Wednesday March 7th at 12:30pm

Some interesting properties of the voter model
Emmanuel Schertzer
Previously, it has been argued, for humans and animals, that social groups containing individuals who are uninformed, or exhibit weak preferences, are particularly vulnerable to the pressure of an extremist minority. However, experiments performed by the Couzin lab suggest that a strongly opinionated minority can dictate group choice, but that the presence of uninformed individuals spontaneously inhibits this process, returning control to the numerical (less strongly opinionated) majority. A natural question is whether those biological observations can be extended to human systems. In this talk, I will investigate the influence of uninformed individuals on the outcome of an election. In order to so, I will first introduce the voter model, a general framework to model the propagation of political opinions. Finally, I will show how the paradigm described above can be related to some well known properties of the random walk.

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Wednesday March 14th at 12:30pm

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota
Vanni Bucci
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can aect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibioticsensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data conrms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups, thus it provides an ecological formalism to help interpret the present surge in microbiome data.

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Wednesday March 21st at 12:30pm

Spring Recess
No lab tea

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Wednesday March 28th at 12:30pm

Faster tree speciation in wet versus dry habitats
Anping Chen
Identifying the mechanisms that generate species diversity patterns has been a central issue in ecology for a long time. In recent years, phylogeography has been an important tool in investigating the origin and maintenance of biodiversity from local to global scales. Most phylogeographical studies focus on phylogenetic relatedness or distance in relation to community structure or environmental gradients. Few explore how the phylogenetic age structure changes along an environmental gradient and its macroevolutionary implications. Here, using forest plot survey data from the Panama Canal watershed and molecular phylogenetic reconstruction, we investigate how average phylogenetic age changes along a rainfall gradient and its possible explanation and potential implications. Data from 48 forest plots in the watershed show a significant negative relationship between average phylogenetic age and precipitation (R2=0.2419, P<0.001) for tree-sized species (breast height diameter > 10cm). In addition, the fraction of species with ages less than 10 MY significantly increases with rainfall (R2=0.2414, P<0.001). Other age thresholds produce similar qualitative results. This decreasing phylogenetic age (or increasing fraction of young species) towards wetter habitats suggests a significant niche difference in macroevolutionary processes and faster speciation in wet versus dry sites. Differences in tree mortality rate and, consequently, community turnover rate could be major drivers of the speciation rate difference in wet versus dry.

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Wednesday April 4th at 12:30pm

The TIM barrel fold as a catalyst of early protein-mediated metabolism
Aaron Goldman
The triosephosphate isomerase (TIM) barrel protein fold is thought to be present as the catalytic domain in an astonishing 10% of all modern enzymes and is known to catalyze five of the six major categories of enzyme function as defined by the Enzyme Commission. Here we explore the possibility that this metabolic ubiquity reflects a fundamental role of TIM barrel enzymes in the origin of protein-based metabolism. We identify ancient TIM barrel enzymes by phylogenetic analysis and show a common ancestry for most of them by sequence profile clustering. These ancient TIM barrel enzymes exhibit the widest observed catalytic range and do so by utilizing a broad range of metal and nucleotide-derived cofactors. These characteristics may reflect the transitional state between prebiotic geochemistry and bona fide metabolism. We offer additional evidence that the expansion of TIM-barrel enzymes took place prior to the development of the DNA genome.

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Wednesday April 11th at 12:30pm

The Fast OR the Furious: Influence of the environment on the burst size vs. latent period trade-off for phytoplankton phages
Juan Bonachela
Phages infecting bacteria have been the focus of an intense study for the last 80 years. Yet, little is known about the viruses that infect phytoplankton. With very limited experimental and theoretical work, the available estimates for key virus traits such as burst size (number of virus replicates per infection event) or latent period (time elapsed between the infection of the host and the release of the replicates) cover several orders of magnitude. On the other hand, theoretical models consider a negligible latent period, overlooking the trade-off that relates it with the burst size. In this Labtea, I will talk about a recently started project in which I want to study how the burst size and latent period are affected by changes in the environment, with the aim of setting the theoretical range of those traits for phytoplankton viruses.

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Wednesday April 18th at 12:30pm

The dynamics of coordinated group hunting and collective information-transfer among schooling prey
Simon Leblanc
In this LabTea, I will present recent work about to be published on the collective dynamics of schooling prey (juvenile Gulf Menhaden) under predation (spotted Seatrout) in their natural shallow estuarine environment (coastal Louisiana). The data collection was made possible by the use of a high resolution sonar providing quality acoustic images over a short range and a with a very fast time scale. We will discuss how information about the predators propagate within prey groups with preys responding directly and indirectly to the threat, how predators coordinate their action during attacks and why they might want to do so.

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Wednesday April 25th at 12:30pm

Testing dynamical predictions of neutral theory against tropical forest data
Ryan Chisholm
Neutral ecological theory accurately predicts static patterns of diversity in high-diversity forests but the dynamic predictions of the theory have received less attention. I will present the results of two dynamical tests of neutral theory against data from tropical forest plots. The first test shows that the rate of input of new species into the 50-ha Barro Colorado Island forest plot is very close to the expected value under neutral theory, suggesting that niche mechanisms do not stabilize species richness at this spatial scale. The second test shows that individual tree species' abundance fluctuations within forest plots are several times larger than predicted by neutral theory, suggesting an important role for temporal niches or for more complex demographic processes. Together, the results inform the ongoing development of parsimonious biodiversity models by point towards the kind of mechanisms that are needed to explain dynamic as well as static biodiversity patterns.

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Wednesday May 2nd at 12:30pm

Phenotypic plasticity and non-additivity in social evolution
Erol Akçay
Some recently developments on social evolution theory alternatively aim to unify and/or overthrow particular types of rules or approaches. Most of these debates revolve around a few issues such as additivity and frequency dependence, and contradictory claims abound. I will discuss a few of the recent attempts to unify behavioral plasticity and population structure in the evolution of cooperation and present some ongoing work that shows some important points tend to get missed in these attempts.

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Wednesday May 9th at 12:30pm

Theoretical effects of fire-nutrient interactions on tree cover in savanna
Adam Pellegrini
While fire has been shown to be a significant factor in tropical savanna ecosystems, the role of nutrient limitation in tropical savanna ecosystems is relatively poorly understood. Fire can volatilize nutrients, especially N, representing a large nutrient loss pathway absent in the forest N-cycle. Here, we examine those potentials in a theoretical model, first by examining the effects of fire on N limitation in a fire-present and fire-absent system, then by examining those effects in the context of fire as a process that is emergent at the landscape scale. We use this modeling approach as an attempt to start to address how feedbacks between fire and nutrient cycles contribute to our understanding of savanna occurrence and stability. Parameterization of the model from empirical results in the literature suggests that certain tropical savanna systems may be especially sensitive to the effects of biogeochemistry on savanna and forest distribution.

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Monday May 21st at 12:30pm

Adaptive Network Structure in the Surveillance of Communicable Livestock Diseases.
Benjamin Morin
We approach a novel extension in the study of communicable livestock diseases (e.g., foot and mouth disease, FMD) by studying a model containing a descriptive treatment of adaptive importing behavior amongst countries engaged in livestock trade. We stylize the behavior of two types of agents for each country: the importing agent and the boarder control agent. The importing agent adjusts his behavior in order to maximize profit over some planning horizon by weighing profit made on livestock from another country with the perceived risk of importing contaminated goods, resulting in a large loss in FMD-free countries. The boarder control agent controls the surveillance measures over ports of entry which are engineered to detect, with a prescribed degree of confidence, the presence of infection. Each agent may adapt their behavior to account for disease prevalence and detection standards of the respective countries of origin of the imports as well as the state of the entire system relative to themselves and the valuation of their own current level of FMD (e.g., the desire to remain FMD-free in countries without the resources to quarantine and cull an outbreak may be greater than in a country which may afford such interventions). We investigate these adaptations in the context of completely connected weighted, directed graphs for diseases similar to FMD.

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Links to previous schedules

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    Fall 2011