Jack Sullivan 

Updated Spring 2025

Biology 545 - Phylogenetics

Syllabus

Readings for alternate Wednesdays

Link to Zoom Lectures (Passcode: 099469)

Lecture Notes & Slides

Lecture 1 - Introduction to Systematics and Phylogenetics. Notes Slides.

Costello et al. (2013). An estimate of current diversity (that focuses on macrobial species).

Locey and Lennon (2016). An estimate of the number of extant microbial species.

Li and Wiens (2023). An estimate of current diversity derived by extrapolating the rate of cryptic species in insects.

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

Quinn (2017). An interesting take on the evolution of the term "cladist."

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

Lecture 4 - Characters: Molecular. Notes Slides.

Edwards et al. (2002). An early example of alignment-free genomic distances used for phylogeny.

Steenwyk & King (2024). A recent discussion on the use of conserved syntenic groups in phylogenomics.

Lecture 5 - Alignment. Notes Slides.

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

Lecture 6B - Optimality Criteria: Maximum Likelihod & Minimum Evolution. Notes Slides.

Lecture 7 - "Algorithmic Approaches" to Tree Building. Notes Slides.

Lecture 8 - Searching Tree Space. Notes Slides.

Lecture 9 - The Importance of Models of Sequence Evolution. Notes Slides.

Links to Recorded Lectures

Thursday, 1/9.

Teusday, 1/14.

Thursday, 1/16.

Tuesday, 1/21.

Thursday, 1/23.

Tuesday, 1/28.

Thursday, 1/30.

Tuesday, 2/4.

Thursday, 2/6.

Tuesday, 2/11.

Thursday, 2/13.

Labs

Link to Zoom Labs (Passcode: 623887)

Lab Orientation

Lab 1 - Alignments.

Lab 2 - Tree Searching and Parsimony.

Data Set.

Problem Sets

Problem Set 1 Answers.

Old Exams

Old Exam 1.