Phylogenetic Methods (PhyloMeth). Spring 2021

UT students may sign up at EEB 587.

Syllabus version: 09:52 AM, 02 March, 2021

Instructor: Brian O’Meara ()

Course website:

Office hours by appointment (and routinely available over slack as well)

What you will learn

This is a modern class in phylogenetic methods. You will learn how to get data, build a tree, use comparative methods, and how to make new methods. More importantly, you will learn why to do all this. You will also learn some best practices – these will be annoying at first, but worth it overall.


  • A laptop on which you can install software (have root / admin access)
    • It’ll be easiest if this is a Mac; less easy is Linux; Windows will be hard
  • A question and some data to answer it
  • GitHub account
  • Slack
  • R
  • And other software we’ll learn about during the course

I am revising a textbook as part of the course * HTML version * PDF

It will be updated as we go, so check back frequently.


Grading will be based on effort and performance. Some of the things will be harder for some students than others just given differences in what they’ve been exposed to so far, and I don’t want to penalize students who are less skilled at R, for example. But I do require that you put in work on this class: work through the exercises, think about the papers, etc. Much of the homework is chewy, so it will take some thought to get through, and you might not be able to do all of this. That’s ok. But ask for help!

These projects should be able to serve as the core for a dissertation chapter or published paper: still requiring more work and writing, but a solid idea with preliminary results.


The class is generally flipped: rather than me droning at the front of the room, I’ll be releasing videos online for you to watch. They will be linked to from this syllabus. In class, talk about what was not clear from the videos about methods, and we’ll dig into that. We can also work on problematic parts of the exercises (you should do most of them before class) and talk about papers.


The class discussion board is public on Slack; you will need the [Slack invite code] to join.

Online option

There is a no-credit online option, as well.


Course made possible by: NSF CAREER grant to O’Meara & ongoing support from the Department of Ecology & Evolutionary Biology, U. of Tennessee, Knoxville.

My goal is to have you learn. If you are having trouble with something in the course, or if there is a topic you just have to learn more about, let me know (email, office hours, online forum, etc.). Faculty often use evaluations at the end of the semester to get info from students so we can improve before the next class, but this does not help you directly. To allow the class to improve while you are taking it, I have created a site for anonymous feedback at (and yes, it is really anonymous). Let me know things that are going well or poorly — both are important. I might not implement all your suggestions, but they will all be read and considered, generally the same day you submit them.

Any student who feels s/he may need an accommodation based on the impact of a disability should contact me privately to discuss specific needs. Please contact the Office of Disability Services at 865-974-6087 in Dunford Hall to coordinate reasonable accommodations for students with documented disabilities.

All relevant University policies (including, but not limited to, policies on academic integrity, attendance, etc.) apply to this course. In the case of any conflict between the policies in this syllabus and University policy, University policy applies. The instructor reserves the right to revise, alter, and/or amend this syllabus as necessary. Students will be notified by email of any such revisions, alterations, and/or amendments.