Spring 2014

Titles and abstracts

Wednesday February 12th at 12:30pm

Fire, Nutrients, Plants and Herbivores in South African Savanna
Lars Hedin
Abstract unavailable.

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Wednesday February 19th at 12:30pm

A game theoretic explanation of biome-specific differences in N2-fixers and fixation
Efrat Shefer
N2-fixation is the principal source of nitrogen (N) to land ecosystem, manifested in vastly different patterns across the biosphere. The abundance of symbiotic N2-fixing trees in all stages of tropical forest development is puzzling in light of their scarcity in temperate and Boreal forests, where they dominate early-successional stages and are out-competed by non-fixers at later stages. This pattern presents a paradox: why individuals that pay the costs of N2-fixation succeed in N-rich tropical forests and why not in N-poor extra-tropical forests. I will show how I used a game-theoretic analysis to find the conditions under which N2-fixation is an evolutionary stable strategy (ESS) and how different strategies of N2- fixation are governed by biome-scale climatic constraints on N cycling. We found that a facultative N2-fixation strategy (the ability to down-regulate N2-fixation in reaction to increased soil N availability) is favored in tropical ecosystems where soil N accumulates fast, and results in long-term coexistence of fixers and non-fixers. In extra-tropical forests slow soil N accumulation make the down-regulation of fixation disadvantageous, and the obligate strategy (with constant fixation rate) is favored, despite its long-term exclusion. Our analyses suggest that biome-scale patterns of N2-fixation can be explained by the indirect effect of climate-dependent N cycling on individual-based strategies.

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Wednesday February 26th at 12:30pm

Causes and consequences of regular spatial patterning in foundation species
Corina Tarnita
The increasing availability of high-resolution satellite imagery over the past decade has shown that highly regular and apparently self-organized vegetation patterns are common in nature, especially in semi-arid rangelands. However, there remains much uncertainty about exactly how these patterns form, and whether they are important in determining the stability and productivity of ecosystems. We're combining mathematical modeling with experimental field studies to understand the causes and consequences of regular pattern formation by "foundation species"-specifically, subterranean termites whose mounds are both uniformly patterned and integral to important ecosystem functions such as nutrient cycling and biomass accumulation. In this talk I will be addressing two broad questions: 1. what combination of biological and physical processes generates and maintains this kind of spatial patterning? and 2. what are the emergent effects of these patterns on the overall productivity of ecosystems and their stability in the face of perturbations such as climatic change and overgrazing?

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Wednesday March 5th at 12:30pm

Geometry shapes evolution of early multicellularity
Eric Libby
The transition from unicellularity to multicellularity marks an important shift in the level of organization and individuality of living organisms. Although this transition has occurred independently dozens of times, early steps remain poorly understood. A recent experiment with the yeast Saccharomyces cerevisiae observed the evolution of self-reproducing groups from single-celled precursors. Interestingly, these self-reproducing groups soon evolved a secondary trait: a higher rate of apoptosis. Since groups divide (reproduce) as a result of cell death, increased apoptosis leads to an increase in the number of groups, i.e. group fitness. In the context of the selective regime such a result is puzzling. How does a trait disadvantageous for individual cell fitness but advantageous for group fitness arise when groups originally formed to increase cell fitness? Here, we show that the geometric organization of the group is key to understanding how such a trait might evolve.

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Tuesday March 11th at 2:00pm

Spatial Evolutionary Games (Special Lab tea)
Rick Durrett
In 1994 Durrett and Levin suggested that the outcome of spatial competition could be predicted from properties of the mean-field PDE which is derived by pretending that adjacent sites were always independent. Using recent work of Cox, Durrett, and Perkins on voter model perturbations, I will show that this is true for evolutionary games of the form 1 + wG, where 1 is a matrix of all 1's and w is small, but one must replace assumption of independent sites by the voter model equilibrium. The take home message is simple: the effect of space is equivalent to simply changing some of the entries in the game matrix.

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Wednesday March 12th at 12:30pm

eSLIME: a novel software system for rapid individual-based modeling
David Borenstein
Developing a new model can often be an arduous task, with development times of weeks or more. Here I present eSLIME, a new-high level programming system for lattice-based ecological modeling. The system consists of a modular back-end interface for designing new behaviors and features, and a hierarchical front-end for model definition. Implementing a new model with existing features requires no software background and can be completed in hours instead of weeks. The system can run on a personal computer or a computing cluster, and is designed to run to high replicate overnight. The framework has support for individual-based (local) discrete processes, global discrete processes and reaction-diffusion solute processes, making it applicable for a variety of ecological and biophysical models at many scales. A feature-complete alpha will be available for evaluation within weeks.

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Wednesday March 19th at 12:30pm

No labtea - spring break
Have a wonderful spring break!

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Wednesday March 26th at 12:30pm

Information Flow on Interaction Networks
Simon Leblanc
Many tasks achieved collectively by groups of animals like bird flocks and fish schools involve gathering, processing and exchanging information. Individuals in a group take decisions based on information that they gather from the environment and from their neighbors who, voluntarily or not, produce information by performing actions which are the results of their own decision process. And apparently, information flows pretty fast in these groups! But the underlying mechanisms are unknown. By modeling this decision process using Bayesian updating and optimizing prior probabilities of individuals' decision process for fast and robust consensus at the group level, independently of the group's structure (which might be dynamic) or one's position on the interaction network, we hope to find general principles of synergetic information processing applicable to a wide range of groups and to groups of any size.

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Wednesday April 2nd at 12:30pm

The maintenance of prey diversity in a stochastic world
Alex Washburne and Jacob Socolar
How will introducing (or removing) a prey-switching predator affect prey diversity? Theoretical studies of infinitely-large and deterministic systems governing predator and prey interactions suggest that a prey-switching predator (a predator that preferentially targets the more abundant prey) should promote diversity among its prey. We use a Gillespie algorithm to create trajectories of non-zero-sum neutral prey communities with migration from a metacommunity, density-dependent birth and constant per-capita probabilities of death. Crucially, these simulations represent communities with finite prey and predator populations, and they capture demographic stochasticity while preserving the same expected trajectories of the underlying ODEs. We use our simulation scheme to explore the influence of prey-switching predators on finite prey populations, and our initial investigations reveal a common answer in biology: it depends. At realistic predation rates, we find that prey-switching predators do promote prey species-richness when the prey carrying capacity is high. However, for low prey carrying capacity, identical predation regimes depress prey diversity. These results are preliminary and our work is far from complete - we're excited to brainstorm with y'all about what of our simulation and its results are novel and interesting for theoreticians, and what would be relevant for wildlife managers. We also invite discussion of the pitfalls and utility the Gillespie algorithm in ecology, which can be easily (yet cautiously) applied to simulate stochastic trajectories of any system of ODEs.

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Wednesday April 2nd at 2:00pm

The evolution of bet-hedging and phenotypic plasticity (Special Lab tea)
Jeremy Van Cleve
In light of an uncertain future, organisms face a difficult trade-off. They can either specialize on a single phenotype across a range of environments, hedge their bets by randomly choosing among a set of phenotypes, or invest in physiological machinery to adjust their phenotype plastically. Understanding the evolutionary relationship between these strategies remains a puzzle. Here, we present a simple model for the evolution of specialization, bet-hedging, and plasticity that reveals how these strategies are fundamentally sensitive to the shape of the cost of plasticity. When costs accelerate with plasticity, bet-hedging is the likely outcome. In contrast, decelerating costs can lead to full adaptive plasticity, but only when initial conditions are right. The shape of the cost curve is due to the genetic and metabolic network machinery underlying plastic traits, which means that certain networks are more likely than others to evolve plasticity.

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Wednesday April 9th at 12:30pm

Biogeochemical controls of symbiotic N2 fixation across broad spatial scales
Sarah Batterman
Symbiotic N2-fixing trees fill a critical role in the nitrogen cycle, yet the abundance of fixers varies widely both within and across biomes. A dominant idea proposed to resolve this variation is that fixation and fixers are controlled by soil phosphorus, although the mechanisms of how fixers depend on phosphorus remain largely unexplored and have different consequences for the distribution of fixers. I will consider four hypotheses about the influence of phosphorus on fixers relative to non-fixers, and examine the consequences of these hypotheses for how fixers differ from non-fixers in phosphatase activity, abundance, and nutrient limitation status across a gradient in phosphorus availability. I use a theoretical plant-soil ecosystem model that includes different ideas about the phosphorus costs of fixation, competitive abilities of fixers relative to non-fixers, and phosphorus uptake strategies. If I have time, I will evaluate the predictions with empirical data from our own work and the literature and new analyses of forest inventory data from tropical forests.

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Wednesday April 16th at 12:30pm

A(nother) bottom-up approach to cooperative governance of risky commons
Vitor Vasconcelos
Despite broad participation, global efforts to curb emissions have failed to achieve tangible results: only a few nations are actually bound to reduce emissions. The trade-off between breadth and depth of commitment begs for a game theoretical approach in modelling decision of nation representatives. In this framework, previous research has shown that local climate governance may be less riddled with barriers to cooperation than global agreements - which has been commonly name as a bottom-up approach. Following this clue, my aim is to more clearly define the different levels in which decisions are made together with the direction of decision propagation and therefore obtain a more realistic bottom-up approach; With it understand if the previous results still hold and potentially get new results. I will focus this talk in presenting some of the previous results and explaining how I aim to upgrade the model.

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Wednesday April 23rd at 12:30pm

Will climate change result in mismatches between fish and phytoplankton phenology? Empirical evidence from the California Current Ecosystem and global Earth System Model (ESM) forecasts
Rebecca Asch
Climate change has prompted an earlier arrival of spring in numerous ecosystems. It is uncertain whether such changes are occurring in Eastern Boundary Current upwelling ecosystems, because these regions are subject to decadal climate oscillations and regional climate models predict seasonal delays in upwelling. To answer this question, the phenology of 43 species of larval fishes was investigated between 1951-2008 in southern California. The first principal component of this dataset showed a progression towards the earlier appearance of larvae. 39% of phenological events indicated increasingly early peaks in larval abundance, while 18% exhibited delayed phenology. These changes were best explained by a secular trend towards earlier warming of surface waters rather than by decadal climate cycles, such as the Pacific Decadal Oscillation and the North Pacific Gyre Oscillation. Species displayed similar changes in phenology at both the decadal scale and the interannual scale associated with El Niño. Species with earlier phenology were characterized by an offshore, epipelagic distribution, while species with delayed phenology were more likely reside in coastal, demersal habitats. Earlier spawning was correlated solely with changes in sea surface temperature (SST). A combination of SST and upwelling were responsible for delays in fish phenology. Since species with earlier phenology were not changing their seasonal abundance synchronously with upwelling and mesozooplankton, they may be increasingly subject to mismatches with their prey in the future. Among species with no long-term phenological trends, a contraction in the length of their spawning season was detected, which could increase recruitment variability.

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Wednesday April 30th at 12:30pm

No lab tea this week.

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May 7th at 12:30pm

The extracellular matrix strongly influences competition in bacterial biofilms
Carey Nadell
Bacteria are now known to be highly interactive organisms that often live in groups, termed biofilms. Cells within a biofilm secrete a variety of extracellular compounds, many of which become part of a matrix that provides structural integrity and stress resistance to the bacterial group as a whole. The biofilm matrix is of central interest not only as a common feature of bacterial collective behaviour, but also as a target for the manipulation of microbial communities in contexts that are either helpful (e.g., probiotic applications and bioremediation) or harmful to humans (e.g., pathogenesis and industrial biofouling). We aim to discover the forces governing biofilm composition with respect to secreted compounds, with an emphasis on the extracellular matrix. Using the model organism Vibrio cholerae, and with tools from molecular genetics and microfluidics, we demonstrate that matrix production confers a strong competitive advantage to matrix-secretors when co-inoculated with non-secretors. However, this advantage is accompanied by an ecological cost: impaired dispersal. We further show that biofilms can resist invasion by planktonic cells, and that different protein components of the matrix are responsible for invasion resistance in different regions of biofilms in accordance with their spatial localization.

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May 7th at 3:00pm in Guyot 100

Introduction to two cultural factors of resilience (cooperation and subsistence) through two fishing markets examples in Solomon Islands (Gizo city and Lau community)
Pierre Hardy, CNRS (French National Centre for Scientific Research)
Socio-economies of fishing markets stands as a complex systems which evolutions within time can be hardly forecast. Factors of changes in such socio-economies are however important to address since they justify the fishing pressure which remains the principal cause of marine biodiversity decline throughout the world. As a matter of fact , relevant models conceptualizations are needed to embrace main possible adaptations. Many economists have integrated individual motivations that rule decision in marine resources' exploitation and consumption in order to propose more accurate models. Although a few have fully invest the cultural aspects that influence individual motivations. Island fishing markets are at stake since they represent most of the time the only source of proteins and rule a major part of the global socio-economy. We believe that cultural influence are even more prevalent in islands and explains evolution of island global socio-economies. Possible future adaptations are constitutive of the resilience of island fishing sectors, they are indeed driven by cultural factors of change, namely cultural factors of resilience. Two cultural factors of resilience will be presented through two multi-agents models within two case study from Solomon Islands. The first one illustrates how cooperation if it becomes part of a cultural change of the next 20 years can prevent from fish stock collapse. The second proves how the cultural changes of the last 40 years have prevent from food security problems. Finally, we will insist on the cultural implication in models' building for better expertise in small scale fishery management in Oceania.

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Wednesday May 14th at 12:30pm

No lab tea this week.

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May 19th at 12:30pm

Second Best Agreements and the Prisoners' Dilemma Trap
Astrid Dannenberg
A critical decision facing international negotiations is how to frame a cooperative agreement. Here we conduct an experimental test of the decision to frame an agreement to supply a public good as a prisoners' dilemma or a coordination game. The prisoners' dilemma framing can potentially sustain a first best outcome, but this outcome cannot be supported as a Nash equilibrium. The coordination game may be able to sustain only a second best outcome, but this outcome can be supported as a Nash equilibrium. We show that groups perform much better in the coordination game than in the prisoners' dilemma. Yet, many groups repeatedly choose the prisoners' dilemma framing, believing that they are making the better choice when they are almost certainly wrong.

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May 21st at 12:30pm

The effect of environmental variance on species diversity
Ryan Chisholm
Theoretically, environmental variance can either increase or decrease species diversity in natural ecosystems. Increased diversity is caused by storage effects, whereas decreased diversity is caused by a higher risk of stochastic extinction. The extent to which each of these mechanisms operates in nature remains unknown. I present data from the Centre for Tropical Forest Science plot network suggesting that the second mechanism is more prevalent, i.e., that sites with higher environmental variability have lower tree species richness. I put this in the context of the empirical and theoretical literature and discuss future avenues towards resolving the effect of environmental variance on biodiversity.

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June 24th at 12:30pm

Explaining and predicting biodiversity patterns in tropical forest tree communities
Tak Fung
Tree communities in tropical rainforests are home to a bewildering array of species, yet they exhibit consistent patterns in the way the abundances of these species are arranged in space and time. My work aims to elucidate the processes underlying some of these patterns, using a mathematical modelling approach. Firstly, I detail how I extended previous analyses of a neutral model to quantify and predict species-abundance distributions for tree communities with dynamics that are not at a steady state. This allows the restrictive assumption of a steady state to be relaxed. Secondly, I detail how I added variation in demographic rates arising from environmental factors to a neutral model, to produce a new model that is capable of accurately capturing static and dynamic patterns of biodiversity in tropical rainforest tree communities. This is an improvement over previous models that could only realistically reproduce static patterns.

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July 1st at 12:30pm

Navigating emerging challenges in marine aquaculture: Toxins, temperature, and new species
Dane Klinger
Global demand for seafood is increasing as a function of more people eating more fish. While catches from wild fisheries have stagnated or declined, aquaculture is poised to increase production to meet growing demand. Marine aquaculture, where fish and other aquatic organisms are farmed in the ocean, is one of several promising means of meeting increasing demand for seafood. However, farming fish in the ocean presents novel problems for aquaculture enterprises. The ocean is an open system, meaning that farmers cannot easily control factors such as water quality or water temperature. I examine two specific challenges in marine aquaculture: 1) the effect of toxins from marine oil spills on juvenile fish and 2) the effect of temperature on digestion efficiency. Finally, marine aquaculture presents an opportunity to culture new species. I model the financial viability and resource intensity of two candidate aquaculture species, bluefin and yellowfin tuna, for which demand is likely to increase in the near future.

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Links to previous schedules

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