Jack Sullivan 

Updated Spring, 2017

Biology 545 - Principles of Systematic Biology

Syllabus

Readings for alternate Mondays

Lecture Notes & Slides

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.

Lab Exercises

Lab 1 - Introduction & Coding Morphological Characters.

Camin and Sokal (1965).

Sokal (1983).

Lab 2 - Alignment.

Data Set

Lab 3 - Parsimony Data Set.

Problem Sets

Problem Set 1. Answers.

Old Exams

Exam 1 Answers to Problems.