Theoretical Ecology Lab Tea

Theoretical Ecology Lab Tea is a forum to present on and discuss theory-driven research in ecology. Talks are 30 minutes and are followed by questions and discussion.

Lab Tea typically meets on Wednesdays at 12:30 pm during the fall and spring semesters in Eno 209.

For the fall semester of 2020, talk schedules and email lists will be maintained by Maddie Andrews and Jacob Levine. Please contact Maddie or Jacob to join the Lab Tea email list.

Fall 2020

Click on an event to view the talk title and abstract

Date and time Speaker
Andreas Mayer
Jamie Lopez
Edward Tekwa
Jacob Levine
Alex Hening
Olivia Prosper
Samniqueka Halsey
Olivia Chu
Kristin Douglass
Thanksgiving
Dan Cooney
Jizhong Zhou

Note: Priority is given to graduate students. A ⊛ symbol next to the speaker's name means that approval is pending for a week and graduate students can still claim the slot.

Titles and abstracts

Early life imprints the hierarchy of T cell clone sizesAndreas Mayer

The adaptive immune system responds to pathogens by selecting clones of cells with specific receptors. While clonal selection in response to particular antigens has been studied in detail, it is unknown how a lifetime of exposures to many antigens collectively shape the immune repertoire. Here, using mathematical modeling and statistical analyses of T cell receptor sequencing data we develop a quantitative theory of human T cell dynamics compatible with the statistical laws of repertoire organization. We find that clonal expansions during a perinatal time window leave a long-lasting imprint on the human T cell repertoire, which is only slowly reshaped by fluctuating clonal selection during adult life. Our work provides a mechanism for how early clonal dynamics imprint the hierarchy of T cell clone sizes with implications for pathogen defense and autoimmunity.

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Modeling the ecology of parasitic plasmidsJaime Lopez

Plasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the profound role they play in modern biotechnology and antibiotic resistance, our understanding of their natural lifestyles is limited. Much of the existing literature focuses on plasmids as accessory elements for bacteria, positing that plasmids are maintained by positive selection. However, recent experimental results have found that plasmids can spread even when they are a burden to the cell, suggesting that plasmids exist as parasites. The existence of parasitic plasmids has substantial implications for both bacterial evolution and the control of antibiotic resistance, but there is little work studying their ecology. In this work, we use mathematical modeling and bioinformatic analyses to explore the ecology of parasitic plasmids. We begin with single plasmid, single species models and find that different modes of HGT can lead to significant differences in dynamics and optimal infection strategies. We then model plasmid coinfection and find a plasmid “tragedy of the commons” in which runaway invasions of plasmids reduces the fitness of the host to arbitrarily low levels. The resolution of this tragedy of the commons lies on a higher level of selection: in metapopulation models, runaway plasmid invasions are limited by HGT barriers between populations. From our models, we derive the predicted distribution of the number of plasmids per genome and find that the distribution of plasmids in a collection of 18,000 genomes is consistent with a model of parasitic plasmids with positive epistasis.

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Modeling the ecology of parasitic plasmidsAndreas Mayer

Plasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the profound role they play in modern biotechnology and antibiotic resistance, our understanding of their natural lifestyles is limited. Much of the existing literature focuses on plasmids as accessory elements for bacteria, positing that plasmids are maintained by positive selection. However, recent experimental results have found that plasmids can spread even when they are a burden to the cell, suggesting that plasmids exist as parasites. The existence of parasitic plasmids has substantial implications for both bacterial evolution and the control of antibiotic resistance, but there is little work studying their ecology. In this work, we use mathematical modeling and bioinformatic analyses to explore the ecology of parasitic plasmids. We begin with single plasmid, single species models and find that different modes of HGT can lead to significant differences in dynamics and optimal infection strategies. We then model plasmid coinfection and find a plasmid “tragedy of the commons” in which runaway invasions of plasmids reduces the fitness of the host to arbitrarily low levels. The resolution of this tragedy of the commons lies on a higher level of selection: in metapopulation models, runaway plasmid invasions are limited by HGT barriers between populations. From our models, we derive the predicted distribution of the number of plasmids per genome and find that the distribution of plasmids in a collection of 18,000 genomes is consistent with a model of parasitic plasmids with positive epistasis.

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Origami for community regime shiftsEd Tekwa

Physicists have long had the luxury of folding space on paper to demonstrate wormholes. Here I show how simple community stability and regime shifts can be understood using papers and pencil, like not by drawing but by cutting and poking holes. Technically it’s a project for coral-macroalgal dynamics but that’s not essential information. And then I will show some data on the global body size-biomass spectrum across taxa, which doesn’t seem directly related to community stability… I think?

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Coexistence of annual plants competing for water in phenologically structured communitiesJacob Levine

The phenological separation of competitors is often hypothesized to regulate their coexistence, though a mechanistic understanding of why phenology influences the outcome of competition is only beginning to develop. In this study we present an analytically tractable model of water competition in Mediterranean annual communities and demonstrate that variation in plant phenology alone can maintain high diversity in a spatially homogeneous, single-resource system. In this model, species differ in their ability to grow in dry conditions and therefore differ in the length of time they can grow due to the nonrenewable supply of water within seasons. We find that infinite diversity is feasible provided a tradeoff between the rate and duration of growth exists.

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Modern Coexistence Theory and Beyond: a general theory of coexistence for ecological communitiesAlex Hening

One of the most fundamental questions from population biology is related to finding out when interacting species coexist. I present results that significantly generalize Chesson's Modern Coexistence Theory to ecosystems of species that interact nonlinearly and are influenced by large stochastic environmental fluctuations. The theory works both for discrete and continuous-time models and yields sharp conditions for coexistence and extinction. I present two applications: 1) the complete classification of three-species stochastic dynamics, 2) the rescue effect stochastic fluctuations can have on species competing for limited resources and how this relates to the Competitive Exclusion Principle from ecology.

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Malaria dynamics within the mosquitoOlivia Prosper

The malaria parasite Plasmodium falciparum requires a vertebrate host and a female Anopheles mosquito to complete a full life cycle, with sexual reproduction occurring in the mosquito. This sexual stage of the parasite life cycle allows for the production of genetically novel parasites. In the meantime, a mosquito’s biology creates bottlenecks in the infecting parasites’ development. We developed a two-stage stochastic model of the generation of parasite diversity within a mosquito, and were able to demonstrate the importance of heterogeneity amongst parasite dynamics across a population of mosquitoes on estimates of parasite diversity. A key epidemiological parameter related to the timing of onward transmission from mosquito to vertebrate host is the extrinsic incubation period (EIP). Using simple models of within-mosquito parasite dynamics fitted to empirical data, we investigated factors influencing the EIP.

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Understanding Disease Emergence Patterns by Exploring Host-tick Associations Samniqueka Halsey

Tick-borne diseases are increasing worldwide and have a progressively negative impact on human health. Effectively managing disease requires enhanced knowledge of the interactions of the tick, its hosts, and the environment. Due to the ongoing expansion of ticks and tick-borne diseases in the United States, there is a need to identify the role wildlife hosts play in the establishment and maintenance of tick populations. After quantifying the patterns of tick and pathogen prevalence relative to wildlife hosts, we developed a spatially explicit individual-based tick interaction model to evaluate vector control strategies. From this, we conclude that effective management efforts should be aimed at multiple stages in the ticks' life cycle and enacted for the long term. We then quantified support for three mechanisms (i.e., vector regulation, encounter reduction, and transmission reduction) through which biodiversity–disease relationships occurred using species richness, Shannon H diversity, and host abundance. For each of the dilution effect mechanisms, host abundance was consistently the best-supported predictor of disease risk. Ultimately, understanding the mechanisms through which the wildlife host community influences pathogen transmission cycles in nature will help foster effective control and reduction of disease risk in humans.

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An adaptive voter model applied to polarization dataOlivia Chu

In human social systems, it is natural to assume that individuals’ behaviors influence and are influenced by their interactions. Mathematically, it is common to study these dynamics on networks, where nodes are individuals and edges between these nodes denote some type of connection. Adaptive network models explore the dynamic relationship between node properties and network topology. Adaptive voter models are one such type of model, in which changes in the network take place through homophily or social learning. In this talk, I will discuss the effects of heterogeneous network re-wiring rules on the dynamics of the adaptive voter model, and present a preliminary framework to incorporate polarization data into this model.

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Social memory and niche construction in a hypervariable environmentKristina Douglass

I will present a new paper forthcoming in the American Journal of Human Biology, in which my colleague Dr. Tanambelo Rasolondrainy and I advocate a closer consideration of the social dimensions of the human niche, and their inextricable links to the biophysical world. Specifically, we explore the theoretical implications of applying a Niche Construction Theory framework to understanding the role of social memory in constructing the human niche of SW Madagascar. We look at how social memory facilitates mobility, resource use, and the creation and maintenance of social identities and ties among communities of foragers, farmers, herders and fishers living under hypervariable climatic conditions. The paleoclimate record of SW Madagascar reflects major fluctuations in climatic conditions over the course of Holocene human settlement. Archaeological evidence derived from surface surveys and excavations demonstrate short-term occupations of sites, suggesting that frequent residential mobility and flexible subsistence strategies have been central features of life on the southwest coast for millennia. Today, despite rapid changes linked to globalization and increasing market integration, mobility remains key to the lives of communities of the region. Based on an oral history survey conducted between 2017-2018 and including over 100 elders from 32 different communities, we argue that social memory and the ability to transmit oral histories of exchange, reciprocity and cooperation, as well as ecological knowledge are key adaptive mechanisms that facilitate mobility and access to resources. We argue that social memory, its maintenance and perpetuation contribute to a niche that makes human lifeways possible in a hypervariable environment. The preservation and transmission of oral histories and ecological knowledge are thus critical to future resilience and sustainability.

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Long-Time Behavior of Nested Replicator Equations for Multilevel SelectionDan Cooney

In this talk, we will explore a model for the evolution of cooperative behaviors in group-structured populations, in which individuals compete with group members for individual-level replication while competition also takes place between groups as a whole. We formulate a differential equation describing the changing composition of cooperators and defectors within groups, and study the conditions under which the long-time behavior of our model favors the individual incentive to or the collective incentive to promote cooperation. We derive conditions under which the population converges to a steady state supporting cooperation. The resulting steady states feature a shadow of the lower-level of competition: when groups are best off with an intermediate level of cooperation, the optimal level of cooperation cannot be achieved even in the limit of infinite strength of between-group competition. We also derive thresholds for the relative selection strength separating regimes in which cooperation persists or goes extinct, and study an extension of our model that allows for the study of coevolution of cooperative strategies and the games that are played within groups.

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Links to previous schedules

  1. Fall 2000
  2. Spring 2001
  3. Fall 2001
  4. Spring 2002
  5. Fall 2002
  6. Spring 2003
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  8. Spring 2004
  9. Fall 2004
  10. Spring 2005
  11. Fall 2005
  12. Spring 2007
  13. Fall 2007
  14. Spring 2008
  15. Fall 2008
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  17. Fall 2009
  18. Spring 2010
  19. Fall 2010
  20. Spring 2011
  21. Fall 2011
  22. Spring 2012
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  25. Fall 2013
  26. Spring 2014
  27. Fall 2014
  28. Spring 2015
  29. Fall 2015
  30. Spring 2016
  31. Fall 2016
  32. Spring 2017
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  34. Spring 2018
  35. Fall 2018
  36. Spring 2019
  37. Fall 2019
  38. Spring and Summer 2020