Phylogenetic Methods (PhyloMeth). Spring 2022

UT students may sign up at EEB 587.

Syllabus version: 09:55 AM, 24 February, 2022

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


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, you’ll be given content to process at home. This material 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 Volunteer Creed reminds us that we bear the torch to give light to others. As Volunteers, we commit to caring for one another and for the members of the communities in which we live, work, and learn.

For your safety and the safety of your fellow student scholars, I ask that you wear a properly fitted mask while in class. This greatly reduces the transmission among residents of our community, helping to end this surge sooner and reduce the potential for another variant. It also reduces the chance that we unknowingly pass the disease to an unvaccinated or immunocompromised individual.

Current CDC guidelines recommend using N95, KN94 or K95 masks, which are the most effective in preventing infection from the current Omicron variant.

Almost all of us prefer to learn face-to-face in a regular classroom setting - it is the core of teaching and learning here at UT. I have structured the in-person class to maximize student learning based on previous semesters. However, as covid surges and absences increase, I will need to balance the needs of in-person students as well as those who temporarily cannot attend (which may include me if I need to quarantine or isolate). In this case, I may make a class-by-class instructional decision to hold class online so that ALL students can learn together. The chance of this should be reduced as covid passes.

The classroom is a shared environment: with a different group of students, or a different instructor, the class could work very differently. It is on all of us to create a classroom where everyone can feel safe, be safe, and learn. To that end, please do not impose a higher degree of risk on people than they themselves are comfortable with. If everyone in your study group is comfortable meeting outside, that’s fine! If one person does not want to, please do not force them. Within the classroom space, many people will be uncomfortable, and be put at higher risk, to be around people without masks. Please show consideration for each other.

Any student may attend class remotely for whatever reason: this is strongly advised for students who are isolating (have covid) or under quarantine (may have been exposed). Remote attendance may also be a good option for students who would prefer not to wear a mask but who want to minimize risk to others.

Please fill out the covid support form if you may need to quarantine or isolate; it will let the campus covid support team give you guidance on next steps, and it also lets UTK track the current state of the pandemic on campus.


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


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 they 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.