Grad Core Phylogenetics 2014

UTK EEB requires new graduate students to take an intensive team-taught course covering ecology and evolution. I present the phylogenetics portion (tree creation and tree use).
Note the anonymous feedback form: Suggest changes while it can still help you in class.

Fall 2014:

This year I am teaching the entire phylogenetics portion. Here is the syllabus (PDF) and lectures are below; the recorded videos are here.

  1. Intro to phylo (PDF), R exercise
  2. Likelihood, Bayes, model selection, bootstrap. (PDF), R exercise, R exercise answers Background reading: Lewis 2001
  3. Ingredients for phylogenetic methods. PDF. Background reading: O’Meara 2012
  4. DNA models, heterogeneity, alignment (PDF). Mesquite, Tracy Heath’s Beast Tutorial
  5. Continuous traits and tree stretching (PDF). R script
  6. Gene tree incongruence. Background reading: Maddison 1997 PDFQuiz
  7. Species, speciation, taxonomy PDF
  8. Diversification PDF

Study Guide
I had three main goals in this section: making sure you know what sort of questions you can address using phylogenies, having some idea of what methods are available (or close to being available, with a little work) to answer these questions, and having the basic understanding to read and know how to build a tree.
Things you won’t have to know: the difference between gamma and kappa, the equation for multivariate normal, authors behind methods, or similar specifics that you’ll forget again in a month. What I do want you to know:

  • How are trees made?
  • Why are trees made?
  • Compare and contrast a phylogram and a chronogram.
  • Given a tree, answer questions about its topology or other features (i.e., what’s the closest relative to X on the tree?).
  • Compare and contrast bootstrapping and Bayesian approaches for understanding uncertainty.
  • What is a continuous time Markov chain with a finite state space?
  • Why do we care about the above?
  • How are models for DNA related to models for a binary morphological trait?
  • Connect the central limit theorem to the multivariate normal. Why does this make sense for an evolutionary model?
  • What is independent contrasts? When would you use this?
  • What are ways to deal with heterogeneity of processes on a tree? Why is this important?
  • What is tree stretching? What questions does this let you ask?
  • What are sister group comparisons used for?
  • What is the difference between Bayesian and likelihood approaches?
  • Compare and contrast hypothesis testing, model selection, and parameter estimation.
  • What are some approaches to understanding diversification?
  • Why are there methods for jointly looking at diversification and trait evolution?
  • Given a certain biological question, I may ask you what sort of approach you would take to it. The various empirical examples should help with this.

Note that this is the content I want you to know, but not necessarily the questions. There would not be time for these to be essay questions, so I will ask for some of this information in short answer questions and just a few essays.