Welcome to the phylogenetics module of Genome Sciences 541.

After this course, I hope you will be able to

• understand basic features of evolutionary trees
• recognize situations when evolutionary thinking is important
• be able to interpret what trees do and do not tell us
• be familiar with the various types of tree inference, and when they are useful
• understand likelihood-based phylogenetic inference as a statistical estimation problem, including what a substitution model is
• understand the choices one makes when performing likelihood-based tree inference
• understand potential pitfalls of tree inference methods
• understand the tools one has to assess confidence in a phylogenetic tree
• understand the impact of recombination on phylogenetic inference
• understand the basics of tree search

Prerequisites

Software prerequisites

• The seaview sequence alignment and phylogenetic analysis tool.
• Anaconda with some core packages. If you don’t already have this set up here are some steps for you:
  • Install Miniconda
  • Historically my recommendation has been (running linux):

conda create --name 541 python=3.11; conda activate 541
conda install jupyter matplotlib pandas scipy
conda install -c bioconda iqtree

• I recently got a M2 mac and so my install process has been:
  • Install iqtree. Note that you’ll have to do this to avoid the “malicious software” block
  • Install Mamba and:

mamba create --name 541 python=3.11; conda activate 541
mamba install jupyter matplotlib pandas scipy

Day 1: Phylogenetics motivation and intro

• Discussion: getting an intuitive grasp of how phylogenetic methods work via interactive doodling
• Discussion: Understanding trees

Day 2: Phylogenetics methods

• Discussion: Phylogenetics motivation
• Perform sequence alignment on sample data using seaview
• Lecture: Phylogenetics methods intro
• Try using various algorithms to build trees with seaview; then try clicking “Full, Swap, Re-root, and Subtree”

Homework 1

• Fill in the blanks in the Homework 1 Jupyter notebook.
• Submit the Jupyter notebook run from scratch (“Restart & Run All”) and exported to PDF. If you have problems exporting to PDF, that’s fine, HTML and .ipynb are also fine formats (with my preference in that order).

Day 3: Sequence alignment, recombination and trees as data structures

• Lecture: introduction to likelihood-based phylogenetics (video)
• Lecture: Phylogenetic confidence measures
• Investigate a mysterious data set using aLRT and bootstrapping
• Lecture: Tree exploration

Day 4: Further topics

• Lecture: Overview of sequence substitution models (video)
• Lecture: Sequence alignment
• Perform sequence alignment of some HIV gag sequences
• Lecture: Trees and recombination
• Testing for recombination using GARD

Homework 2

• Fill in the blanks in the Homework 2 Jupyter notebook.
• Submit the Jupyter notebook run from scratch (“Restart & Run All”) and exported to PDF. If you have problems exporting to PDF, that’s fine, HTML and .ipynb are also fine formats (with my preference in that order).

Books

• Inferring Phylogenies by Felsenstein
• The Phylogenetic Handbook edited by Lemey, Salemi, and Vandamme, chapters by the stars

Introductory lecture series (this is really good!)

• Introduction to likelihood-based phylogenetics video (with slides)
• Introduction to phylogenetic models video (with slides)
• Introduction to Bayesian statistics and how it is used in phylogenetics (with slides)
• More Bayesian phylogenetics: proposals, prior distributions, hierarchical models, and Bayes factors (with slides)

Software

• FastTree – approximate ML
• RAxML, PhyML, and IQ-TREE – somewhat less approximate ML
• BEAST – Bayesian, inferring event times and rooted trees
• MrBayes and RevBayes – Bayesian, inferring unrooted trees
• DataMonkey, your one-stop online shop for selection and recombination analysis