Jack Sullivan 

Updated Spring, 2013

Biology 545 - Principles of Systematic Biology

Syllabus

Readings

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

Lecture 2 - The History of Phylogenetics: Notes Slides.

Lecture 3 - Characters: Homology, Morphology: Notes Slides.

Lecture 4 - Characters: Molecular: Notes Slides.

Lecture 5 - Alignment Notes Slides.

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

Lecture 6B - Optimality Criteria: ML & ME: 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 - Substitution Models: Notes Slides.

Lecture 11 - Increasing Model Complexity: Notes Slides.

Lecture 12 - Model Selection: Notes Slides.

Lecture 13 - Method Performance: Notes Slides.

Lecture 14 - Support: Consensus, Decay & Bootstrap: Notes Slides.

Lecture 15 - Support: Jackknife & Bayesian Nodal Probabilities: Notes Slides.

Lecture 16 - Hypothesis Testing: Notes Slides.

Lecture 17 - Molecular Clocks: Notes Slides.

Lecture 18 - Multiple Data Sets: Supermatrices, Supertrees, Partitions and Mixtures Notes Slides.

Lecture 19 - Species-Tree Estimation: Notes Slides.

Lecture 20 - Taxon Sampling: Notes Slides.

Lab 1 - Coding Morphology & Intro to Unix.

Lab 2 - Alignment.

Data set.

Lab 3 - Parsimony & PAUP*

Data Set

Lab 4 - Maximum Likelihood, GARLi & BEAST

Config File for GARLi

Lab 5 - Assessing Nodal Support

Problem Set 1 Answers

Old Exam 1

Problem Set 2 Answers

Old Exam 2