About this course
Acknowledgements
1
Course background
1.1
Learning objectives
1.2
Existing resources
1.3
Course overview: map of modules
2
Why theory?
2.1
Theory for conceptual insight
2.2
Theory for prediction
2.3
Insight and prediction for real applications
3
Start simple
3.1
Equilibrium theory of island biogeography
3.2
Neutral theory of biodiversity
4
Simple metrics for summarizing theoretical ecological predictions
4.1
Species richness
4.2
Species abundance
4.3
Hill numbers
5
Introducing the Rules of Life Engine
5.1
Simulating the neutral theory of biodiversity with the RoLE model
5.2
Prelude: who would we test this theory with real data?
6
Competitive coexistence theory
6.1
Simulating modern competitive coexistence theory with the RoLE model
6.2
Prelude: where do fitness and competitive differences come from?
7
Briefest of introductions to model testing
7.1
Exploritory analysis
7.2
What is likelihood
7.3
Model fitting with likelihood
7.4
Model comparison with likelihood
7.5
Beyond likelihood
8
Testing the netural theory and competitive coexistence
8.1
Exploritory analysis
8.2
Fitting the models to data
8.3
Comparing model support
9
Solving biodiversity paradoxes by exploring deeper time patterns
9.1
Temporal dynamics can help distinguish ecological processes
9.2
Ecological processes derive from evolutionary processes
9.3
Evolutionar processes derive from ecological processes
9.4
Prelude: how can we model eco-evolutionary feedbacks?
10
Introduction to modeling macroevolutionary processes
10.1
Modeling phylogenies
10.2
Modeling evolving traits
11
Introduction to modeling macroevolutionary processes
11.1
Modeling phylogenies
11.2
Modeling evolving traits
12
Modeling evolving phylogenies and traits with the Rules of Life Engine
12.1
Modeling phylogenies
12.2
Modeling evolving traits
13
Introduction to modeling microevolutionary processes
13.1
The coalescent
13.2
Modeling genetic variation
13.2.1
Mutations
13.2.2
Neutral drift
13.2.3
Selection
13.2.4
Immigration
14
Simple metrics for summarizing theoretical population genetic predictions
14.1
Genetic diversity
14.2
Hill numbers
15
Modeling neutral molecular evolution with the Rules of Life Engine
16
Reintroducing the Rules of Life Engine to model eco-evolutionary feedbacks
16.1
Why feedbacks are hard
16.2
Doing it with RolE
17
Using the Rules of Life Engine to analyze eco-evolutionary data
18
Miscellaneous stuff
18.1
Coalescent approach to neutral model
18.2
Spatial patterns and processes
19
Applying eco-evolutionary theory
19.1
Re-framing applied questions as theoretical questions
19.2
Case study: Habitat fragmentation
19.3
Case study: Climate change
19.4
Case study: Invasion
19.5
Case study: Working landscapes
Theory in ecology and evolution with applications for a changing world
Module 15
Modeling neutral molecular evolution with the Rules of Life Engine
Do it