# Ecological Dynamics (Fall, 2017)

## Info

- Class time/location: MW 3:00-4:15 in COB2 170
- Discussion section: W 1:00-2:20 in SSM 104

- Office hours: SE1 288, MW 9-10 AM
- Syllabus
- Topical schedule

Readings for the course will be provided below. However, if you are new to theoretical biology, the following resources may prove helpful. The following code identifies the level at which the book is aimed: (B: Beginner; I: Intermediate; A: Advanced). These are must-have resources if you plan to do a lot of theory!

*A Primer of Ecology*: Nicholas J. Gotelli (B)*Mathematical Biology I,II*: J.D. Murray (I/A)*Theoretical Biologists Toolbox*: Marc Mangel (B/I)*Nonlinear Dynamics and Chaos*: Steven Strogatz (B/I)*Quantitative Conservation Biology*: W.F. Morris, D.F. Doak (B/I)*The Ecological Detective*: Marc Mangel (B/I)*The Art of Modeling Dynamic Systems*: F. Morrison (I)

About the final project

The final project will feature a problem that you investigate using tools from the course, but related to your own research. The gold standard would be something that can add to your thesis, or serve as a publisheable side project down the road. The idea will be to articulate an interesting question in your domain of expertise, find a way to investigate that question using tools from the course, and exploring the implications, etc. At the end of the course, you will give a formal presentation to the class in the form of a professional meeting talk (15-20 min) that gives us background, explanation of methods, and results. I’m available during office hours if you want to chat about ideas, techniques, etc.

Due Wednesday, October 18: A paragraph describing what you want to do, and the possible methods that you might use to investigate the problem

## Readings

- 17/08/23: Theoretical Biologist’s Toolbox 1 (Mangel)
- 17/08/28: Theoretical Biologist’s Toolbox 2 (Mangel)
- 17/08/30: Nonlinear Dynamics and Chaos 1 (Strogatz)
- 17/09/06: Nonlinear Dynamics and Chaos 2 (Strogatz)
- 17/09/22: Generalized Modeling of Ecological Population Dynamics (pgs 1-6)
- 17/10/04: Nonlinear Dynamics and Chaos 3 (Strogatz)
- 17/10/11: R. May, Nature 1972; S. Allesina, PopEcol 2015
- 17/10/19: S. Schreiber, Ecology 2011
- 17/10/30: Kondoh, Science 2003; Valdovinos, EcolLett 2010

## Notes

- Discrete population growth
- Continuous population growth and linear stability analysis
- More linear stability analyisis and intro to bifurcations
- Bifurcations: Saddle node and Transcritical
- Pitchfork bifurcations, hysteresis, and spruce budworms
- Generalized modeling: 1D systems
- Analysis of 2-D systems
- Eco-evolutionary dynamics
- Adaptive foraging
- Canonical Equation for Activity Choice
- Canonical Equation for Activity Choice: Part 2
- Canonical Equation for Allocation Processes

## Code

- Spatial and temporal variation (.nb)
- Logistic map (.nb)
- Fixed point analysis (.nb)
- Niche Model (.R)
- Dynamic food webs (.R); you need this function too (.R)
- Extinction experiments (.R)
- Eco-evolutionary dynamics
- Adapative foraging (.nb)
- Canonical equation for activity choice (with forward sims)

## Cool stuff to check out

## Coding resources

- R
- Julia
- Other