Jack Sullivan 

Updated Spring, 2015

Biology 545 - Principles of Systematic Biology

Syllabus

Revised Lecture Schedule.

Readings

Problem Set 1 Answers.

Problem Set 2 Answers.

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

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

Lecture 3 - Characters: Homology, 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: Minimum Evolution and Maximum Likelihood. Notes Slides.

Lecture 7 - "Algorithmic" Approaches. Notes Slides.

Lecture 8 - Searching Tree Space. Notes Slides.

Lecture 9 - The Importance of Models. Notes Slides.

Lecture 10 - Models of Nucleotide Substitution. Notes Slides.

Lecture 11 - Among-Site Rate Variation. Notes Slides.

Lecture 12 - Model Choice. Notes Slides.

Lecture 13 - Performance of Methods. Notes Slides.

Lecture 14 - Nodal Support. Notes Slides.

Lecture 15 - Hypothesis Testing. Notes Slides.

Lecture 16 - Molecular Clocks. Notes Slides.

Lecture 17 - Multiple Data Sets. Notes Slides.

Lecture 18 - Species Trees. Notes Slides.

Lab 1 - Introduction to UNIX, Coding.

Camin and Sokal (1965).

Sokal (1983).

Lab 2 - Alignment. Data Set.

Lab 3 - Tree Searching. Data Set.

Lab 4 - Maximum Likelihood and Bayesian Estimation.

Lab 5 - Nodal Support and Posterior Distributions.

Old Exam 1. Key.

Old Exam 2. Key.