Zach will try to create and post some questions after each lecture. These questions are optional, and are tools you can use to gauge your understanding of the material from lecture and help guide your studying.

Lecture 3 - 25 Jan 2022

Consensus Trees

  • What are the differences between strict, semi-strict, and majority rule consensus trees?
  • What is a rogue taxon, and what do rogue taxa have to do with maximum agreement subtrees?


  • Who was Willi Hennig? How does his phylogenetic method differ from parsimony, and what is the main issue it cannot overcome?
  • Who were Charles Michener and Robert Sokal and what was their contribution to the field of phylogenetics? They had a different name to their work though, what is it?
  • Who were Anthony Edwards and Luca Cavalli-Sforza? What was their contribution to Phylogenetics? Why didn’t their likelihood analysis work?
  • Who were Joseph Camin and Robert Sokal, and how does their method differ from true parsimony.
  • What type of data did the first molecular tree rely on, and why wasn’t it DNA? (Hint: Think about Fred Sanger)
  • In what circumstances might you use ordered characters and when might you use unordered characters?
  • What is a constant site and how does it differ from an variable site? What does this have to do with parsimony?
  • Make sure you can explain how parsimony works with a small tree. What do steps have to do with parsimony, and what is the principle of parsimony?
  • What do transitions and transversions have to do with a nucleotide substitution matrix? (this is something we’ll learn more about next week)

Lecture 4 - 27 Jan 2022


  • Make sure you can make phylogentic trees from splits (Re: Homework 1)

Parsimony Continued

  • What would a step matrix look like if we don’t count transitions, but we weight transversions from purines to pyrimidines 2 times more than transversions from pyrimidines to purines.
  • What are the differences between synapomorphic, autapomorphic, and symplesiomorphic character states? Draw a simple tree and indicate in which taxa the above characters states would be present.
  • Can you think of another word from evolution which describes homoplasy?
  • What are the consistency and retention indexes? How are they used in the context of parsimony trees?

Distance Methods (Least Squares and Minimum Evolution)

  • If you perform a distance analysis (LS/ME), will your results (tree length) be specific to a given tree topology, a given character, or both?
  • How does SplitsTree differ from a normal phylogenetic tree? What can this tell you about the tree?

Lecture 5 - 01 Feb 2022

Review (from lab)

  • What is a star tree, and what does it have to do with a neighbor joining tree?

Exploring Models

  • Why do we use models? Be able to complain model complexity and model fit.

Jukes-Cantor 1969

  • How many parameters does this model have? What are the model parameter(s) and what are the assumptions we invoke when we use this model? Can you make a substitution matrix for this model?
  • What do branch lengths (edge lengths) represent? What parameters do we use to calculate them – why is it impossible to calculate these parameters de novo?
  • Say we are calculating a transition probability for a nucleotide substitution on a site from a G to a T. Before this site had a G nucleotide, the nucleotide was an A. How does this change how we go about calculating transition probabilities when using a Markov model?

Lecture 6 - 03 Feb 2022


  • What are the differences between the different models (JC69, K80(K2P), F81, HKY85, GTR). How many paramaters do they have, what are they?
  • Be able to explain the concept of nested models. When comparing models, why would the nexted nature of models be important?
  • What is a basic explaination of rate heterogeneity? (Will be explained in greater detail later in the semester)