Welcome to M.Biodiv.441 Evolutionary Ecology!

Here you can find the complete documentation of the course.

Check out the Schedule for details about the timeline.

Attention

The 🔓 password for unlocking the files will be given in class.

And here are some important usage notes, check out Usage for more:

Note

Note boxes highlight goals and achievements of the course/week/day. Pay attention to them.

ExercisesQuestions of the Day

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Content

• Introduction
  • Course Structure
  • Major Goals
• How to Sample
  • Sampling accessoires
  • Habitat of oribatid mites
  • How to sample meadows and grasslands
  • What’s the best time to sample oribatid mites?
  • What shall I do with my plastic bag full of „dirt“?
  • What happens to my samples?
• Species Identification
• First Week
  • Major Goals
  • Monday
    • Tasks of the Day
  • Tuesday
    • Tasks of the Day
  • Wednesday
    • Tasks of the Day
  • Thursday
    • Tasks of the Day
  • Friday
    • Homework
• Second Week
  • Major Goals
  • Monday
    • Tasks of the Day
  • Tuesday
    • Tasks of the Day
  • Wednesday
    • Tasks of the Day
  • Thursday
    • Tasks of the Day
  • Friday
    • Tasks of the Day
• Third Week
  • Major Goals
  • 🧬Mini research project🧬
  • Monday
    • Summary
    • Tasks of the Day
  • Tuesday
    • Tasks of the Day
  • Wednesday
    • Tasks of the Day
  • Thursday
    • Tasks of the Day
  • Friday
    • Tasks of the Day
• Schedule
• Sections
  • Geneious Prime
    • Working with Geneious Prime
    • Export Data
  • Database and Search Strategies
  • Downloading and Saving
  • Sequence Editing
  • Models of Sequence Evolution
    • jModelTest 2 (Darriba et al. 2012)
    • How to compute likelihoods of models of sequence evolution
    • Set up the analysis
    • Comparing likelihoods using AIC and BIC
    • Saving your results
  • How to Infer Phylogenetic Trees
    • Neighbor Joining (NJ)
  • How To Draw Phylogenetic Trees
  • Maximum Likelihood
    • RAxML (Randomized Accelerated Maximum Likelihood, Stamatakis 2006)
    • Settings in RAxML
    • Start RAxML
    • RAxML results
  • Bayesian Inference
    • MrBayes (Huelsenbeck and Ronquist, 2001)
    • Before Starting MrBayes
    • Parameter Settings and Help
    • Defining the Model of Sequence Evolution
    • Setting Priors
    • Starting the Analysis
    • Stopping or Pausing the Analysis
    • Writing a batch file (optional)
    • Posterior Analysis
    • MrBayes Results
  • Ape package
  • Getting Started with R
• Lectures
• Usage