Jack Sullivan 

Updated Spring, 2017

Biology 545 - Principles of Systematic Biology

Syllabus

Readings for alternate Mondays

Lecture Notes & Slides

Talk

Lecture 1. Introduction & Importance of Systematics. Notes Slides.

Pauly et al. (2009). The authors point out that taxonomic changes should only be made when current groups are found to be non-monophyletic.

Patterson & Norris (2016) The authors argue for a taxonomic revision for a group based on equivalency of ranks (in this case, genera).

Lecture 2. The History of Phylogenetic Inference. Notes Slides.

Lecture 3. Characters: Homology and Morphology. Notes Slides.

Lecture 4. Characters: Molecular. Notes Slides.

Lecture 5. Alignment. Notes Slides.

Lecture 6A. Introduction to Trees and Optimality Criteria: Parsimony. Notes Slides.

Lecture 6B. Optimality Criteria: Maximum Likelihood and Minimum Evolution. Notes Slides.

Lecture 7. Algorithmic Approaches. Notes Slides.

Lecture 8. Searching Tree Space. Notes Slides.

Lecture 9. Why Models Matter. Notes Slides.

Lecture 10. Models of Sequence Evolution. Notes Slides.

Lecture 11. Modeling Among-site Rate Variation. Notes Slides.

Lecture 12. Model Selection. Notes Slides.

Lecture 13. Performance of Methods. Notes Slides.

Lecture 14. Consensus and Nodal Support. Notes Slides.

Lecture 15. Hypothesis Testing. Notes Slides.

Lecture 16. Molecular Clocks. Notes Slides.

Lecture 17. Partitioned and Mixture Models. Notes Slides.

Lecture 18. Species-tree Estimation. Notes Slides.

Lab Exercises

Lab 1 - Introduction & Coding Morphological Characters.

Camin and Sokal (1965).

Sokal (1983).

Lab 2 - Alignment.

Data Set

Lab 3 - Parsimony Data Set.

Lab 4 - Model-based Methods.

Lab 5 - Nodal Support.

Problem Sets

Problem Set 1. Answers.

Problem Set 2. Answers.

Old Exams

Exam 1 Answers to Problems.

Exam 2 (with key).